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]
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Variant: NM_016239.4(MYO15A):c.1582G>A (p.Gly528Ser)

CA8423128

504629 (ClinVar)

Gene: MYO15A
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: b6ea399d-f7a0-4cd2-b814-7e0bd870f57c
Approved on: 2021-07-22
Published on: 2022-05-13

HGVS expressions

NM_016239.4:c.1582G>A
NM_016239.4(MYO15A):c.1582G>A (p.Gly528Ser)
NC_000017.11:g.18120382G>A
CM000679.2:g.18120382G>A
NC_000017.10:g.18023696G>A
CM000679.1:g.18023696G>A
NC_000017.9:g.17964421G>A
NG_011634.1:g.16677G>A
NG_011634.2:g.16677G>A
ENST00000647165.2:c.1582G>A
ENST00000205890.9:c.1582G>A
ENST00000583079.1:n.1215G>A
ENST00000615845.4:c.1582G>A
NM_016239.3:c.1582G>A

Likely Benign

Met criteria codes 2
BP4 BS1_Supporting

Evidence Links 0

Expert Panel

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 64/23748) of the c.1582G>A (p.Gly528Ser) variant in the MYO15A gene is 0.217% for African/African-American chromosomes by gnomAD, 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). Additionally, computational prediction analysis using the metapredictor tool REVEL suggests that the variant may not impact the protein (BP4). 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_Supporting, BP4.
Met criteria codes
BP4
REVEL score of 0.017, which is meets the threshold to apply BP4 (<0.15). Not well conserved in UCSC (4 mammals have different amino acid at this residue).
BS1_Supporting
The filtering allele frequency (the lower threshold of the 95% CI of 64/23748) of the c.1582G>A (p.Gly528Ser) variant in the MYO15A gene is 0.217% for African/African-American chromosomes by gnomAD, 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).
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