# Structural Variation **URL:** https://discuss.gnomad.broadinstitute.org/c/structural-variation/8.md [Latest](https://discuss.gnomad.broadinstitute.org/latest.md) · [Categories](https://discuss.gnomad.broadinstitute.org/categories.md) · [Tags](https://discuss.gnomad.broadinstitute.org/tags.md) --- ## [About the Structural Variation category](https://discuss.gnomad.broadinstitute.org/t/about-the-structural-variation-category/14)
**Author:** [@kchao](https://discuss.gnomad.broadinstitute.org/u/kchao)\ **Replies:** 0
Any questions about structural variants belong in this category. --- ## [Urgent query - discrepancy between SVs v2.1 & SVs v4.1: missing hemizygotes in the larger dataset](https://discuss.gnomad.broadinstitute.org/t/urgent-query-discrepancy-between-svs-v2-1-svs-v4-1-missing-hemizygotes-in-the-larger-dataset/839)
**Author:** [@Gyorgy\_Fenyofalvi](https://discuss.gnomad.broadinstitute.org/u/Gyorgy_Fenyofalvi)\ **Replies:** 2\ **Last updated:** [July 6, 2026, 4:19pm UTC](https://discuss.gnomad.broadinstitute.org/t/urgent-query-discrepancy-between-svs-v2-1-svs-v4-1-missing-hemizygotes-in-the-larger-dataset/839 "2026-07-06T16:19:54Z")
Hello, This duplication (DMD exons 56-60) is reported in the two datasets with the same size & breakpoints: GnomAD SVs v2.1 has 1 female carrier, and 6 hemizygotes (which is quite unlikely statistically). While in… --- ## [Filtering the v4 Exome CNV VCF](https://discuss.gnomad.broadinstitute.org/t/filtering-the-v4-exome-cnv-vcf/842)
**Author:** [@leajp](https://discuss.gnomad.broadinstitute.org/u/leajp)\ **Replies:** 0\ **Last updated:** [July 1, 2026, 1:28pm UTC](https://discuss.gnomad.broadinstitute.org/t/filtering-the-v4-exome-cnv-vcf/842 "2026-07-01T13:28:28Z")
Hello, I am filtering the v4 Exome CNV VCF to get the final list of 66,903 rare CNVs. The original vcf file has 68,699 rows (variants), but when I filter it on the FILTER-column (keeping only “PASS”) I get 67,952 varia… --- ## [Best practices for filtering Manta SV calls before comparison with gnomAD-SV?](https://discuss.gnomad.broadinstitute.org/t/best-practices-for-filtering-manta-sv-calls-before-comparison-with-gnomad-sv/838)
**Author:** [@Veronique\_Geoffroy](https://discuss.gnomad.broadinstitute.org/u/Veronique_Geoffroy)\ **Replies:** 0\ **Last updated:** [June 9, 2026, 11:58am UTC](https://discuss.gnomad.broadinstitute.org/t/best-practices-for-filtering-manta-sv-calls-before-comparison-with-gnomad-sv/838 "2026-06-09T11:58:47Z")
Hello, We are working with a cohort of ~800 WGS samples and have generated SV calls using Manta. For downstream analyses, we annotate each SV according to whether a matching event is observed in gnomAD-SV. One concern … --- ## [Centromeric DEL detected by Manta and visible in coverage, but missing from gnomAD-SV](https://discuss.gnomad.broadinstitute.org/t/centromeric-del-detected-by-manta-and-visible-in-coverage-but-missing-from-gnomad-sv/833)
**Author:** [@Veronique\_Geoffroy](https://discuss.gnomad.broadinstitute.org/u/Veronique_Geoffroy)\ **Replies:** 2\ **Last updated:** [June 6, 2026, 1:22pm UTC](https://discuss.gnomad.broadinstitute.org/t/centromeric-del-detected-by-manta-and-visible-in-coverage-but-missing-from-gnomad-sv/833 "2026-06-06T13:22:36Z")
Hello, I am analyzing structural variants in a WGS cohort and have encountered a deletion that raises some questions regarding the gnomAD-SV filtering process. The variant is a DEL on chr11:54,756,310–54,778,113 (GRCh3… --- ## [Homozygotes enrichment in repeated regions](https://discuss.gnomad.broadinstitute.org/t/homozygotes-enrichment-in-repeated-regions/832)
**Author:** [@MathisB](https://discuss.gnomad.broadinstitute.org/u/MathisB)\ **Replies:** 0\ **Last updated:** [May 31, 2026, 4:06pm UTC](https://discuss.gnomad.broadinstitute.org/t/homozygotes-enrichment-in-repeated-regions/832 "2026-05-31T16:06:50Z")
Hello, We have noticed that some structural variants in certain subpopulations were particularly enriched in homozygotes within repeated regions, for exemple DEL\_CHR15\_C65ED383, DEL\_CHR15\_3430BA77 and DEL\_CHR15\_FD0D5513… --- ## [BLK duplication variants](https://discuss.gnomad.broadinstitute.org/t/blk-duplication-variants/565)
**Author:** [@abdullah\_sezer](https://discuss.gnomad.broadinstitute.org/u/abdullah_sezer)\ **Replies:** 2\ **Last updated:** [May 4, 2026, 3:04pm UTC](https://discuss.gnomad.broadinstitute.org/t/blk-duplication-variants/565 "2026-05-04T15:04:08Z")
Some structural variants in gnomAD SVs v4.1.0 such as DUP\_CHR8\_77D3CCE7, DUP\_CHR8\_0DFC84AB, and DUP\_CHR8\_5D05B234 show detectable allele counts in the population data. However, the database also indicates homozygous indi… --- ## [Structural variants](https://discuss.gnomad.broadinstitute.org/t/structural-variants/805)
**Author:** [@stephane](https://discuss.gnomad.broadinstitute.org/u/stephane)\ **Replies:** 1\ **Last updated:** [May 4, 2026, 2:58pm UTC](https://discuss.gnomad.broadinstitute.org/t/structural-variants/805 "2026-05-04T14:58:33Z")
Dear members of gnomAD, We are investigating structural variation in a repetitive region on human chromosome 15. In the SVs v4.1.0 database, we identified two sets of deletion variants - one comprising three calls and t… --- ## [Skewed sex distribution of SVs in PAR1](https://discuss.gnomad.broadinstitute.org/t/skewed-sex-distribution-of-svs-in-par1/804)
**Author:** [@mattle1990](https://discuss.gnomad.broadinstitute.org/u/mattle1990)\ **Replies:** 2\ **Last updated:** [May 4, 2026, 2:51pm UTC](https://discuss.gnomad.broadinstitute.org/t/skewed-sex-distribution-of-svs-in-par1/804 "2026-05-04T14:51:35Z")
Hi, We are interested in the DHRSX gene, located in the pseudoautosomal region of X/Y chromosomes and recently were contacted with a case of a heterozygous deletion encompassing Exon 2. There are two deletions of a simi… --- ## [SV download not matching online browser](https://discuss.gnomad.broadinstitute.org/t/sv-download-not-matching-online-browser/811)
**Author:** [@anagy](https://discuss.gnomad.broadinstitute.org/u/anagy)\ **Replies:** 4\ **Last updated:** [April 14, 2026, 8:31pm UTC](https://discuss.gnomad.broadinstitute.org/t/sv-download-not-matching-online-browser/811 "2026-04-14T20:31:50Z")
Hello! We are using the latest gnomAD SV download (gs://gcp-public-data–gnomad/release/4.1/genome\_sv/gnomad.v4.1.sv.sites.vcf.gz) and have noticed that some of the data included in there is not in the online browser. For… --- ## [GnomAD SVs v4 - discrepancy between hemizygote & male (XY) counts](https://discuss.gnomad.broadinstitute.org/t/gnomad-svs-v4-discrepancy-between-hemizygote-male-xy-counts/340)
**Author:** [@Gyorgy\_Fenyofalvi](https://discuss.gnomad.broadinstitute.org/u/Gyorgy_Fenyofalvi)\ **Replies:** 15\ **Last updated:** [April 6, 2026, 8:16pm UTC](https://discuss.gnomad.broadinstitute.org/t/gnomad-svs-v4-discrepancy-between-hemizygote-male-xy-counts/340 "2026-04-06T20:16:09Z")
Greetings gnomAD CNV team, First, thank you for all your hard work, and for the roll out of gnomAD SVs v4. Recently we have noticed a discrepancy in the numbers between hemizygote counts and male (XY) counts on the X-c… --- ## [Genotype quality for SV call in v4](https://discuss.gnomad.broadinstitute.org/t/genotype-quality-for-sv-call-in-v4/765)
**Author:** [@Rowena\_Mitchell](https://discuss.gnomad.broadinstitute.org/u/Rowena_Mitchell)\ **Replies:** 1\ **Last updated:** [November 26, 2025, 9:18pm UTC](https://discuss.gnomad.broadinstitute.org/t/genotype-quality-for-sv-call-in-v4/765 "2025-11-26T21:18:33Z")
Hi, I am hoping for some advice on the GnomAD v4 SV entry: DEL\_CHR10\_FD5D2313. This variant has a Pass on the filtering stage indicating it is a high quality call, and a quality score of 76. I have been unable to find o… --- ## [Urgent query-Genotype Quality for SVs in gnomAD v4.1.0](https://discuss.gnomad.broadinstitute.org/t/urgent-query-genotype-quality-for-svs-in-gnomad-v4-1-0/770)
**Author:** [@GemmaB](https://discuss.gnomad.broadinstitute.org/u/GemmaB)\ **Replies:** 3\ **Last updated:** [November 20, 2025, 2:24pm UTC](https://discuss.gnomad.broadinstitute.org/t/urgent-query-genotype-quality-for-svs-in-gnomad-v4-1-0/770 "2025-11-20T14:24:02Z")
Hi, We are currently performing an urgent review of a BRIP1 deletion (encompassing exon 8) and was wondering if you could help us understand the quality scores for SVs in gnomAD v4.1.0. We believe our variant overlaps … --- ## [Gene Deletions as LOF?](https://discuss.gnomad.broadinstitute.org/t/gene-deletions-as-lof/775)
**Author:** [@chrisvulpe](https://discuss.gnomad.broadinstitute.org/u/chrisvulpe)\ **Replies:** 2\ **Last updated:** [November 19, 2025, 9:24pm UTC](https://discuss.gnomad.broadinstitute.org/t/gene-deletions-as-lof/775 "2025-11-19T21:24:39Z")
I am looking at the UGT2B7 gene which is known to have a lot of clinically relevant deletions which take out the whole gene but Gnomad doesnt seem to count these as LOF. I was wondering if there is any way to find these… --- ## [SV breakpoints -- are they grouped? How are they determined?](https://discuss.gnomad.broadinstitute.org/t/sv-breakpoints-are-they-grouped-how-are-they-determined/129)
**Author:** [@mkcwong](https://discuss.gnomad.broadinstitute.org/u/mkcwong)\ **Replies:** 2\ **Last updated:** [September 14, 2025, 11:09am UTC](https://discuss.gnomad.broadinstitute.org/t/sv-breakpoints-are-they-grouped-how-are-they-determined/129 "2025-09-14T11:09:43Z")
Hello! Are SV variants with multiple similar (close by) breakpoints grouped together into one variant? If so, how are the breakpoints determined? For example, DEL\_CHR15\_942499A6 with explicit breakpoints of 15:43602626… --- ## [Clarification on a 117-bp deletion variant DEL\_CHR11\_B8445432](https://discuss.gnomad.broadinstitute.org/t/clarification-on-a-117-bp-deletion-variant-del-chr11-b8445432/727)
**Author:** [@jaeseung](https://discuss.gnomad.broadinstitute.org/u/jaeseung)\ **Replies:** 1\ **Last updated:** [August 19, 2025, 3:32pm UTC](https://discuss.gnomad.broadinstitute.org/t/clarification-on-a-117-bp-deletion-variant-del-chr11-b8445432/727 "2025-08-19T15:32:26Z")
Hi, I have a question regarding a 117-bp deletion variant designated DEL\_CHR11\_B8445432 in v4 and DEL\_11\_115846 in v2. I have a case with a similar deletion, but ours is a 132-bp deletion with same rightside breakpoint… --- ## [The positions of two deletions are identical. Why weren’t they merged into a single entry?](https://discuss.gnomad.broadinstitute.org/t/the-positions-of-two-deletions-are-identical-why-weren-t-they-merged-into-a-single-entry/680)
**Author:** [@mitsuhashi](https://discuss.gnomad.broadinstitute.org/u/mitsuhashi)\ **Replies:** 1\ **Last updated:** [August 19, 2025, 3:09pm UTC](https://discuss.gnomad.broadinstitute.org/t/the-positions-of-two-deletions-are-identical-why-weren-t-they-merged-into-a-single-entry/680 "2025-08-19T15:09:14Z")
Hello. The position of DEL\_CHR11\_3DCD2FD1 and DEL\_CHR11\_F213CF06 are identical. Why weren’t they merged into a single entry? Can I merge them? Position11:134738783-134739009 gnomAD gnomAD I found similar cases as fol… --- ## [Is there a data dictionary for the gnomad v4 Structural Variant bed file?](https://discuss.gnomad.broadinstitute.org/t/is-there-a-data-dictionary-for-the-gnomad-v4-structural-variant-bed-file/605)
**Author:** [@RScott](https://discuss.gnomad.broadinstitute.org/u/RScott)\ **Replies:** 1\ **Last updated:** [May 27, 2025, 3:32pm UTC](https://discuss.gnomad.broadinstitute.org/t/is-there-a-data-dictionary-for-the-gnomad-v4-structural-variant-bed-file/605 "2025-05-27T15:32:59Z")
As title, is there any resource that describes the contents of each field in the Structural Variant bed file? --- ## [Third common allele](https://discuss.gnomad.broadinstitute.org/t/third-common-allele/643)
**Author:** [@M.Bloemendal](https://discuss.gnomad.broadinstitute.org/u/M.Bloemendal)\ **Replies:** 1\ **Last updated:** [May 6, 2025, 10:08pm UTC](https://discuss.gnomad.broadinstitute.org/t/third-common-allele/643 "2025-05-06T22:08:36Z")
Most genomic variant studies compare most common variant allele with second common one. Are there studies comparing the second with the third common one, and are third common ones available in the gnomAd database? --- ## [MCNV reference copy states in chr X and chr Y](https://discuss.gnomad.broadinstitute.org/t/mcnv-reference-copy-states-in-chr-x-and-chr-y/590)
**Author:** [@EmmaV](https://discuss.gnomad.broadinstitute.org/u/EmmaV)\ **Replies:** 1\ **Last updated:** [March 5, 2025, 11:14pm UTC](https://discuss.gnomad.broadinstitute.org/t/mcnv-reference-copy-states-in-chr-x-and-chr-y/590 "2025-03-05T23:14:25Z")
Hi, I have a question regarding multiallelic CNVs. In my work, I’m aiming to represent each MCNV as a DEL and a DUP, summing the allele frequencies from each copy state into two new totals. For autosomal chromosomes it … --- ## [Missing END2 in Gnomad SVs VCF](https://discuss.gnomad.broadinstitute.org/t/missing-end2-in-gnomad-svs-vcf/575)
**Author:** [@Benjamin\_Blankenmeis](https://discuss.gnomad.broadinstitute.org/u/Benjamin_Blankenmeis)\ **Replies:** 1\ **Last updated:** [February 20, 2025, 10:05pm UTC](https://discuss.gnomad.broadinstitute.org/t/missing-end2-in-gnomad-svs-vcf/575 "2025-02-20T22:05:26Z")
Hello! I’m using the public gnomad sites VCF as input to another tool (gatk SVConcordance) and received an error about missing END2 in the VCF: Bad input: Attributes END2 and CHR2 are required for BND and CTX records I… --- ## [PhyloP indel scores](https://discuss.gnomad.broadinstitute.org/t/phylop-indel-scores/436)
**Author:** [@Courtney\_Shearer](https://discuss.gnomad.broadinstitute.org/u/Courtney_Shearer)\ **Replies:** 1\ **Last updated:** [February 13, 2025, 9:55pm UTC](https://discuss.gnomad.broadinstitute.org/t/phylop-indel-scores/436 "2025-02-13T21:55:43Z")
Hi I am looking at this indel and others: how are the phyloP scores determined for sites spanning more than 1 bp? max min, mean, or median score? --- ## [Figure broken in SV gnomAD 4 post](https://discuss.gnomad.broadinstitute.org/t/figure-broken-in-sv-gnomad-4-post/536)
**Author:** [@Isobel\_Howard](https://discuss.gnomad.broadinstitute.org/u/Isobel_Howard)\ **Replies:** 1\ **Last updated:** [January 31, 2025, 4:56pm UTC](https://discuss.gnomad.broadinstitute.org/t/figure-broken-in-sv-gnomad-4-post/536 "2025-01-31T16:56:47Z")
Hi there, In the gnomAD v4 page on structural variation, figure 1 with the counts from each population appears to be broken. If this could be reposted so I could refernce it, it would be great. Structural Variants in g… --- ## [Quality score in gnomAD SVs v4.1.0](https://discuss.gnomad.broadinstitute.org/t/quality-score-in-gnomad-svs-v4-1-0/515)
**Author:** [@ocg](https://discuss.gnomad.broadinstitute.org/u/ocg)\ **Replies:** 1\ **Last updated:** [December 18, 2024, 5:59pm UTC](https://discuss.gnomad.broadinstitute.org/t/quality-score-in-gnomad-svs-v4-1-0/515 "2024-12-18T17:59:39Z")
Hi! When looking up variants in the browser to annotate my own variants, is it recommended to only consider SVs of a minimum Quality score (ex: ignore SVs with quality score = 1)? I cannot find this information in the d… --- ## [How to merge multiple variants into the same CNV?](https://discuss.gnomad.broadinstitute.org/t/how-to-merge-multiple-variants-into-the-same-cnv/491)
**Author:** [@A\_Y](https://discuss.gnomad.broadinstitute.org/u/A_Y)\ **Replies:** 0\ **Last updated:** [November 13, 2024, 8:20am UTC](https://discuss.gnomad.broadinstitute.org/t/how-to-merge-multiple-variants-into-the-same-cnv/491 "2024-11-13T08:20:12Z")
For example, 4\_DUP, with 108 individuals carrying this variant.The position of 4\_DUP is Position\[1:925634-966359\],and the vcf file shows POSMIN=911848;POSMAX=948034;ENDMIN=939558;ENDMAX=982191. I am curious about how to… --- ## [GnomAD SVs v4, X-chromosome: homozygous males](https://discuss.gnomad.broadinstitute.org/t/gnomad-svs-v4-x-chromosome-homozygous-males/438)
**Author:** [@Gyorgy\_Fenyofalvi](https://discuss.gnomad.broadinstitute.org/u/Gyorgy_Fenyofalvi)\ **Replies:** 1\ **Last updated:** [November 5, 2024, 7:28pm UTC](https://discuss.gnomad.broadinstitute.org/t/gnomad-svs-v4-x-chromosome-homozygous-males/438 "2024-11-05T19:28:47Z")
Hello, On the X-chromosome there are some homozygotes displayed for males (which doesn’t make sense), and it also gets counted into the overall number of homozygotes. This only seems to be a problem for CNVs (and not fo… --- ## [Gnomad structural variants bed file](https://discuss.gnomad.broadinstitute.org/t/gnomad-structural-variants-bed-file/259)
**Author:** [@christopherlee](https://discuss.gnomad.broadinstitute.org/u/christopherlee)\ **Replies:** 11\ **Last updated:** [September 4, 2024, 8:47pm UTC](https://discuss.gnomad.broadinstitute.org/t/gnomad-structural-variants-bed-file/259 "2024-09-04T20:47:48Z")
For the GRCh38 v4 structural variants, can we get a BED file similar to the one provided for GRCh37 v2 structural variants? Then we could use our existing track build procedures to have a track at UCSC too. Thanks, --- ## [V4.1 Structural Variants BED files](https://discuss.gnomad.broadinstitute.org/t/v4-1-structural-variants-bed-files/402)
**Author:** [@Gerardo\_Perez](https://discuss.gnomad.broadinstitute.org/u/Gerardo_Perez)\ **Replies:** 1\ **Last updated:** [July 29, 2024, 10:05pm UTC](https://discuss.gnomad.broadinstitute.org/t/v4-1-structural-variants-bed-files/402 "2024-07-29T22:05:16Z")
We noticed that the gnomad.v4.1.sv.sites.bed.gz and the gnomad.v4.1.sv.non\_neuro\_controls.sites.bed.gz files have the same number of lines. Is this expected? Also, we noticed that for the v4.1 release there is a non\_neur… --- ## [Genotype quality for assessing CNV in gnomAD SV v4?](https://discuss.gnomad.broadinstitute.org/t/genotype-quality-for-assessing-cnv-in-gnomad-sv-v4/297)
**Author:** [@chenyang1005](https://discuss.gnomad.broadinstitute.org/u/chenyang1005)\ **Replies:** 1\ **Last updated:** [July 22, 2024, 9:53pm UTC](https://discuss.gnomad.broadinstitute.org/t/genotype-quality-for-assessing-cnv-in-gnomad-sv-v4/297 "2024-07-22T21:53:38Z")
I hope to get help on understanding “genotype quality” for one CNV entry in gnomAD v4 (DUP\_CHRY\_97F6D979; \[gnomAD\]). We have transitioned to use Illumina Global Diversity Array (GDA) for our CMA analysis for one year. P… --- ## [SV genotype quality threshold](https://discuss.gnomad.broadinstitute.org/t/sv-genotype-quality-threshold/308)
**Author:** [@louisjanuel](https://discuss.gnomad.broadinstitute.org/u/louisjanuel)\ **Replies:** 1\ **Last updated:** [June 20, 2024, 7:16pm UTC](https://discuss.gnomad.broadinstitute.org/t/sv-genotype-quality-threshold/308 "2024-06-20T19:16:25Z")
Dear gnomAD people, Thank you very much for offering this forum and for your responsiveness to the questions asked, which is of great help to everyone. Maybe I didn’t search well enough, but I couldn’t find where you e… [Next page](https://discuss.gnomad.broadinstitute.org/c/structural-variation/8.md?page=1)