Evidence Repository
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_206933.4(USH2A):c.14419G>A (p.Ala4807Thr)

CA246980

198366 (ClinVar)

Gene: USH2A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: c1d605e5-67f2-43d5-8643-a70536da96b7
Approved on: 2024-02-21
Published on: 2024-04-01

HGVS expressions

NM_206933.4:c.14419G>A
NM_206933.4(USH2A):c.14419G>A (p.Ala4807Thr)
NC_000001.11:g.215648691C>T
CM000663.2:g.215648691C>T
NC_000001.10:g.215822033C>T
CM000663.1:g.215822033C>T
NC_000001.9:g.213888656C>T
NG_009497.1:g.779706G>A
NG_009497.2:g.779758G>A
ENST00000307340.8:c.14419G>A
ENST00000674083.1:c.14419G>A
ENST00000307340.7:c.14419G>A
NM_206933.2:c.14419G>A
NM_206933.3:c.14419G>A
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Uncertain Significance

Met criteria codes 1
PM2_Supporting
Not Met criteria codes 25
BS2 BS4 BS3 BS1 BP2 BP3 BP1 BP4 BP5 BP7 BA1 PVS1 PS2 PS4 PS3 PS1 PP4 PP1 PP2 PP3 PM3 PM1 PM4 PM5 PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2, KCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The variant NM_206933.4:c.14419G>A in USH2A is a missense variant predicted to cause substitution of alanine by threonine at amino acid 4807 (p.Ala4807Thr). The filtering allele frequency (the upper threshold of the 95% CI of 5/30782) of the c.14419G>A variant in USH2A is 0.00006365 for South Asian chromosomes by gnomAD v2.1.1, which is lower than the ClinGen Hearing Loss VCEP threshold (<0.00007) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM2_Supporting (ClinGen Hearing Loss VCEP specifications version 2; 2/21/2024).
Met criteria codes
PM2_Supporting
ExAC MAF of 0.03% in South Asian. 0.016% in gnomAD. http://gnomad.broadinstitute.org/variant/1-215822033-C-T
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
ExAC MAF of 0.03% in South Asian. 0.016% in gnomAD. http://gnomad.broadinstitute.org/variant/1-215822033-C-T
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
ExAC MAF of 0.03% in South Asian. 0.016% in gnomAD. http://gnomad.broadinstitute.org/variant/1-215822033-C-T
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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