Tandem Repeat: PRE-MIR7-2

Short Tandem Repeat
1

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 a (TTTG)₄ repeat to (TTTG)₃.

All 33 subjects annotated as having 3 repeat units still have four TTTG repeats. However, they do have a deletion of the TTTC sequence preceding the STR (15-88569429-TTTTC-T [GRCh38]; rs1456817951). This is a more common variant that is not linked to hypothyroidism.

Thanks!

2

Thank you for pointing this out.

We need to mark those 33 genotypes as “low quality” on manual review, fix how the pathogenic threshold is shown in the histograms, and fix the STRchive link.

https://gnomad.broadinstitute.org/short-tandem-repeat/PRE-MIR7-2?dataset=gnomad_r4