# Latest **URL:** https://discuss.gnomad.broadinstitute.org/latest.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) --- ## [Welcome to gnomAD! 👋](https://discuss.gnomad.broadinstitute.org/t/welcome-to-gnomad/5)
**Author:** [@system](https://discuss.gnomad.broadinstitute.org/u/system)\ **Replies:** 0\ **Last updated:** [June 27, 2023, 4:03pm UTC](https://discuss.gnomad.broadinstitute.org/t/welcome-to-gnomad/5 "2023-06-27T16:03:31Z")
We are so glad you joined us. gnomAD A place for users of the Genome Aggregation Database to discuss the data, ask questions, and get help from eachother and the gnomAD team. Please note, we have a small team so it c… --- ## [Missing variant?](https://discuss.gnomad.broadinstitute.org/t/missing-variant/859)
**Author:** [@JAb](https://discuss.gnomad.broadinstitute.org/u/JAb)\ **Replies:** 1\ **Last updated:** [September 23, 2026, 8:51pm UTC](https://discuss.gnomad.broadinstitute.org/t/missing-variant/859 "2026-09-23T20:51:23Z")
Hi there, Could someone please explain to me why SNV 12-51916114-T-G is present in gnomAD v4.1.1 (allele count 0) but 12-51916114-T-C and 12-51916114-T-A in the same nucleotide are not? Thanks! --- ## [BRCA1 gene page fails to load tonight](https://discuss.gnomad.broadinstitute.org/t/brca1-gene-page-fails-to-load-tonight/852)
**Author:** [@Susan\_WL](https://discuss.gnomad.broadinstitute.org/u/Susan_WL)\ **Replies:** 3\ **Last updated:** [September 10, 2026, 6:03pm UTC](https://discuss.gnomad.broadinstitute.org/t/brca1-gene-page-fails-to-load-tonight/852 "2026-09-10T18:03:21Z")
Tonight the BRCA1 gene page will not load for me. I have tried repeatedly over the course of the evening and it fails every time, showing only the message “Unable to load gene.” What fails: Direct URL: gnomAD Same URL… --- ## [Missing Data in your database](https://discuss.gnomad.broadinstitute.org/t/missing-data-in-your-database/856)
**Author:** [@Ahmed\_Nawzad\_Hasan](https://discuss.gnomad.broadinstitute.org/u/Ahmed_Nawzad_Hasan)\ **Replies:** 1\ **Last updated:** [September 9, 2026, 3:28pm UTC](https://discuss.gnomad.broadinstitute.org/t/missing-data-in-your-database/856 "2026-09-09T15:28:26Z")
Dear recipient, I really appreciate your website gnomAD, it helps researchers, clinicians, etc. I just have a question as we are working on a project about PDCD1 gene sequencing, I cannot understand why there is a miss… --- ## [Variant search - HGVS support](https://discuss.gnomad.broadinstitute.org/t/variant-search-hgvs-support/853)
**Author:** [@ps209497](https://discuss.gnomad.broadinstitute.org/u/ps209497)\ **Replies:** 0\ **Last updated:** [September 9, 2026, 10:07am UTC](https://discuss.gnomad.broadinstitute.org/t/variant-search-hgvs-support/853 "2026-09-09T10:07:29Z")
First, thank you for the amazing gnomAD project — it is an essential resource for all of us working with variants! The problem of understanding different HGVS representations, including RefSeq transcripts and HGVS conse… --- ## [Gnomad WGS AFs are often ~10x the Gnomad WES AF](https://discuss.gnomad.broadinstitute.org/t/gnomad-wgs-afs-are-often-10x-the-gnomad-wes-af/851)
**Author:** [@stu2](https://discuss.gnomad.broadinstitute.org/u/stu2)\ **Replies:** 0\ **Last updated:** [September 2, 2026, 9:48am UTC](https://discuss.gnomad.broadinstitute.org/t/gnomad-wgs-afs-are-often-10x-the-gnomad-wes-af/851 "2026-09-02T09:48:53Z")
Hi all, First, apologies for the cross-posting - I’ve posted this in Biostars but couldn’t get to the bottom of it. I am trying to investigate population allele frequencies from Gnomad v4.1 but I have found that I can’… --- ## [MPC v4.1.1 transcript count in paper differs from score file](https://discuss.gnomad.broadinstitute.org/t/mpc-v4-1-1-transcript-count-in-paper-differs-from-score-file/849)
**Author:** [@Gerardo\_Perez](https://discuss.gnomad.broadinstitute.org/u/Gerardo_Perez)\ **Replies:** 0\ **Last updated:** [August 27, 2026, 3:12am UTC](https://discuss.gnomad.broadinstitute.org/t/mpc-v4-1-1-transcript-count-in-paper-differs-from-score-file/849 "2026-08-27T03:12:58Z")
Hello, We noticed a difference between the MPC v4.1.1 preprint and the downloadable score file. The preprint (https://doi.org/10.1101/2024.04.11.588920), Methods \> Transcripts, states: “For high quality transcripts, … --- ## [Service overloaded](https://discuss.gnomad.broadinstitute.org/t/service-overloaded/800)
**Author:** [@AP715](https://discuss.gnomad.broadinstitute.org/u/AP715)\ **Replies:** 5\ **Last updated:** [August 25, 2026, 7:58am UTC](https://discuss.gnomad.broadinstitute.org/t/service-overloaded/800 "2026-08-25T07:58:06Z")
Anyone having this issue in Chrome or Safari? Its a hit or miss on how long it takes for the data to eventually populate on the page after refreshing several times. --- ## [gnomAD v4.1 cohort inclusion](https://discuss.gnomad.broadinstitute.org/t/gnomad-v4-1-cohort-inclusion/834)
**Author:** [@Fred\_Zhou](https://discuss.gnomad.broadinstitute.org/u/Fred_Zhou)\ **Replies:** 1\ **Last updated:** [August 11, 2026, 9:45pm UTC](https://discuss.gnomad.broadinstitute.org/t/gnomad-v4-1-cohort-inclusion/834 "2026-08-11T21:45:08Z")
Hi all, I am checking allele frequencies and would like to compare them with those from other datasets. I remember that there was previously information available on which cohorts or datasets were included in the gnomA… --- ## [Finding SNV's associated with common diseases](https://discuss.gnomad.broadinstitute.org/t/finding-snvs-associated-with-common-diseases/847)
**Author:** [@David\_Moskowitz](https://discuss.gnomad.broadinstitute.org/u/David_Moskowitz)\ **Replies:** 0\ **Last updated:** [August 7, 2026, 7:12pm UTC](https://discuss.gnomad.broadinstitute.org/t/finding-snvs-associated-with-common-diseases/847 "2026-08-07T19:12:39Z")
I’m a primary care physician trying to integrate genomics into my clinical practice. A patient with early Alzheimer’s disease (so-called “Mild Cognitive Impairment”) with \<1st percentile hippocampal volume and elevated s… --- ## [HGDP 1kG call set phasing information](https://discuss.gnomad.broadinstitute.org/t/hgdp-1kg-call-set-phasing-information/843)
**Author:** [@Karl](https://discuss.gnomad.broadinstitute.org/u/Karl)\ **Replies:** 1\ **Last updated:** [August 7, 2026, 6:43pm UTC](https://discuss.gnomad.broadinstitute.org/t/hgdp-1kg-call-set-phasing-information/843 "2026-08-07T18:43:54Z")
Dear gnomAD team, Thanks for your efforts and your great work. I downloaded the HGDP + 1KG callset. Looking at the data, I see the genotype being reported as e.g., ‘0/0’, which, I understand, indicates unphased data. … --- ## [gnomAD v5 - planned release?](https://discuss.gnomad.broadinstitute.org/t/gnomad-v5-planned-release/845)
**Author:** [@NM-G08](https://discuss.gnomad.broadinstitute.org/u/NM-G08)\ **Replies:** 3\ **Last updated:** [August 5, 2026, 2:43pm UTC](https://discuss.gnomad.broadinstitute.org/t/gnomad-v5-planned-release/845 "2026-08-05T14:43:23Z")
Hello, I heard in some recent meetings that there is going to be a gnomAD v5, and noticed a few topics in here that indicated that the change from v4 to v5 is based only on All of Us Research data being incorporated. I… --- ## [GroupMax values missing for a lot of variants](https://discuss.gnomad.broadinstitute.org/t/groupmax-values-missing-for-a-lot-of-variants/250)
**Author:** [@JJM](https://discuss.gnomad.broadinstitute.org/u/JJM)\ **Replies:** 10\ **Last updated:** [August 4, 2026, 4:32pm UTC](https://discuss.gnomad.broadinstitute.org/t/groupmax-values-missing-for-a-lot-of-variants/250 "2026-08-04T16:32:34Z")
I’d like to understand why GroupMax values are missing for so many variants. For example, among the \>5000 BRCA2 variants in gnomAD, nearly 3000 have GrpMax missing. Most variants are exceedingly rare, leading me to think… --- ## [Tandem Repeat: PRE-MIR7-2](https://discuss.gnomad.broadinstitute.org/t/tandem-repeat-pre-mir7-2/747)
**Author:** [@Helmut\_Grasberger](https://discuss.gnomad.broadinstitute.org/u/Helmut_Grasberger)\ **Replies:** 2\ **Last updated:** [August 2, 2026, 11:32am UTC](https://discuss.gnomad.broadinstitute.org/t/tandem-repeat-pre-mir7-2/747 "2026-08-02T11:32:59Z")
Hello, In the pathogenic STR subset of gnomAD, the pathogenic variant causing congenital hypothyroidism (“Tandem Repeat: PRE-MIR7-2”; OMIM: CHNG3) is incorrectly annotated. The pathogenic variant is the contraction of … --- ## [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… --- ## [Missense constraint updated in v4.1.1?](https://discuss.gnomad.broadinstitute.org/t/missense-constraint-updated-in-v4-1-1/841)
**Author:** [@Marissa\_Ellingson](https://discuss.gnomad.broadinstitute.org/u/Marissa_Ellingson)\ **Replies:** 0\ **Last updated:** [June 29, 2026, 3:47pm UTC](https://discuss.gnomad.broadinstitute.org/t/missense-constraint-updated-in-v4-1-1/841 "2026-06-29T15:47:41Z")
Hello, The gnomAD v4.0 gene constraint announcement stated that “v4.0 metrics are still experimental. We recommend that anyone using the v4.0 constraint results should consider the metric to be in a beta stage, and anyo… --- ## [Quantifying not-normal reported variant frequencies](https://discuss.gnomad.broadinstitute.org/t/quantifying-not-normal-reported-variant-frequencies/840)
**Author:** [@BRENO\_MUNOZ](https://discuss.gnomad.broadinstitute.org/u/BRENO_MUNOZ)\ **Replies:** 0\ **Last updated:** [June 27, 2026, 3:20pm UTC](https://discuss.gnomad.broadinstitute.org/t/quantifying-not-normal-reported-variant-frequencies/840 "2026-06-27T15:20:34Z")
Hi! I’m trying to use gnomAD 3.1 to quantify the not normal frequencies of variants. In that sense, my general idea is that given one variant, e.g. A827G, I want to substract the counts corresponding to the studies comin… --- ## [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 … --- ## [My Java version is: openjdk version "18" 2022-03-22](https://discuss.gnomad.broadinstitute.org/t/my-java-version-is-openjdk-version-18-2022-03-22/836)
**Author:** [@Laurent777](https://discuss.gnomad.broadinstitute.org/u/Laurent777)\ **Replies:** 0\ **Last updated:** [June 7, 2026, 12:36pm UTC](https://discuss.gnomad.broadinstitute.org/t/my-java-version-is-openjdk-version-18-2022-03-22/836 "2026-06-07T12:36:40Z")
My Java version is: openjdk version “18” 2022-03-22. Before I install, my notes say to use Java 11. Is Java 18 going to work? Thanks in advance. L --- ## [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… --- ## [Gnomad V4.1.1 Update Missing Constraint Metrics from V4.1.0](https://discuss.gnomad.broadinstitute.org/t/gnomad-v4-1-1-update-missing-constraint-metrics-from-v4-1-0/830)
**Author:** [@Amy\_Zheng](https://discuss.gnomad.broadinstitute.org/u/Amy_Zheng)\ **Replies:** 1\ **Last updated:** [May 28, 2026, 8:45pm UTC](https://discuss.gnomad.broadinstitute.org/t/gnomad-v4-1-1-update-missing-constraint-metrics-from-v4-1-0/830 "2026-05-28T20:45:03Z")
Hi! We’re working on a project using the constraint metrics (specifically missense and synonymous o/e) provided by Gnomad. However, we recently noticed that the constraint tables displayed in V4.1.0 are no longer availa… --- ## [V4.1.1 variant md5sums outdated](https://discuss.gnomad.broadinstitute.org/t/v4-1-1-variant-md5sums-outdated/829)
**Author:** [@christopherlee](https://discuss.gnomad.broadinstitute.org/u/christopherlee)\ **Replies:** 2\ **Last updated:** [May 27, 2026, 9:03pm UTC](https://discuss.gnomad.broadinstitute.org/t/v4-1-1-variant-md5sums-outdated/829 "2026-05-27T21:03:43Z")
The md5sums listed for both the exomes and genomes v4.1.1 variants files are instead the md5sums for the v4.1 files. Can I get verification that the links are correct to the v4.1.1 files and have the updated m5sums built… --- ## [Feedback from using the GraphQL API for ClinPGx](https://discuss.gnomad.broadinstitute.org/t/feedback-from-using-the-graphql-api-for-clinpgx/825)
**Author:** [@Ryan\_Whaley](https://discuss.gnomad.broadinstitute.org/u/Ryan_Whaley)\ **Replies:** 0\ **Last updated:** [May 19, 2026, 7:05pm UTC](https://discuss.gnomad.broadinstitute.org/t/feedback-from-using-the-graphql-api-for-clinpgx/825 "2026-05-19T19:05:00Z")
Hi, I’ve got some feedback and questions about using the gnomAD API to pull basic frequency data. For background, I’m a developer at ClinPGx. We’ve used gnomAD v2 and v3 data in our system for a while and we want to pul… --- ## [Stratified coverage counts for gnomAD v4](https://discuss.gnomad.broadinstitute.org/t/stratified-coverage-counts-for-gnomad-v4/814)
**Author:** [@crowlands](https://discuss.gnomad.broadinstitute.org/u/crowlands)\ **Replies:** 1\ **Last updated:** [May 12, 2026, 8:59pm UTC](https://discuss.gnomad.broadinstitute.org/t/stratified-coverage-counts-for-gnomad-v4/814 "2026-05-12T20:59:17Z")
Hi gnomAD team, Thanks for continuing to maintain such an essential resource. As part of an approach to combine in-house sequencing data with gnomAD summary data, we want to identify variant positions with significantl… --- ## [Presentation on misconceptions about gnomAD](https://discuss.gnomad.broadinstitute.org/t/presentation-on-misconceptions-about-gnomad/824)
**Author:** [@kchao](https://discuss.gnomad.broadinstitute.org/u/kchao)\ **Replies:** 0\ **Last updated:** [May 12, 2026, 3:35pm UTC](https://discuss.gnomad.broadinstitute.org/t/presentation-on-misconceptions-about-gnomad/824 "2026-05-12T15:35:56Z")
Missed our recent talk on common misconceptions about gnomAD? Watch the recording covering what the resource is, what metadata are available, and the types of studies it includes. --- ## [Mapping Quality and Pseudogene Interference](https://discuss.gnomad.broadinstitute.org/t/mapping-quality-and-pseudogene-interference/823)
**Author:** [@NM-G08](https://discuss.gnomad.broadinstitute.org/u/NM-G08)\ **Replies:** 0\ **Last updated:** [May 8, 2026, 7:43pm UTC](https://discuss.gnomad.broadinstitute.org/t/mapping-quality-and-pseudogene-interference/823 "2026-05-08T19:43:25Z")
Hello, I’m trying to better understand the reliability of allele frequencies in the gnomAD database from a variant curation perspective. Many genes have pseudogenes, and I was wondering if there is some quality metric … --- ## [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… [Next page](https://discuss.gnomad.broadinstitute.org/latest.md?page=1)