Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_206933.3(USH2A):c.7167C>T (p.Ser2389=)

CA1394924

681822 (ClinVar)

Gene: USH2A (HGNC:7399)

Condition: Usher syndrome (MONDO:0019501)

Inheritance Mode: Autosomal recessive inheritance

UUID: 0f97b706-2a00-4fce-8bbe-6744fe0a63bc

Approved on: 2020-05-26

Published on: 2020-05-26

HGVS expressions

NM_206933.3(USH2A):c.7167C>T (p.Ser2389=)

NM_206933.3:c.7167C>T

NC_000001.11:g.215934749G>A

CM000663.2:g.215934749G>A

NC_000001.10:g.216108091G>A

CM000663.1:g.216108091G>A

NC_000001.9:g.214174714G>A

NG_009497.1:g.493648C>T

NG_009497.2:g.493700C>T

NM_206933.2:c.7167C>T

NM_206933.4:c.7167C>T

ENST00000307340.7:c.7167C>T

Likely Benign

BP7 BP4 BS1_Supporting

Evidence Links 0

Expert Panel

Hearing Loss VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Hearing Loss VCEP

The filtering allele frequency (the lower threshold of the 95% CI of 57/19928 of the c.7167C>T (p.Ser2389=) variant in the USH2A gene is 0.22% for East Asian chromosomes by gnomAD v2.1.1, which is a higher frequency than would be expected for an autosomal recessive pathogenic variant based on the thresholds defined by the ClinGen Hearing Loss Expert Panel (BS1_Supporting). The silent c.7167C>T variant in USH2A is not predicted by the computational prediction analysis using MaxEntScan to impact splicing (BP4, BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BS1_P, BP4,BP7.

BP7

no splicing impact predicted by MaxEntScan and other splicing predictors in Alamut.

BP4

Residue is not highly conserved and no splicing impact predicted by MaxEntScan and other splicing predictors in Alamut.

BS1_Supporting

The filtering AF (95% CI) is 0.22% (57/19928) of East Asian chromosomes in gnomAD v2.1.1 and 0.22% (12/3114) of South Asian chromosomes in gnomAD v3.

Curation History

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