rs786200882
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Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1PP5
The NM_153700.2(STRC):c.3156_3157insC(p.Cys1053LeufsTer20) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 12)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
STRC
NM_153700.2 frameshift
NM_153700.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.19
Genes affected
STRC (HGNC:16035): (stereocilin) This gene encodes a protein that is associated with the hair bundle of the sensory hair cells in the inner ear. The hair bundle is composed of stiff microvilli called stereocilia and is involved with mechanoreception of sound waves. This gene is part of a tandem duplication on chromosome 15; the second copy is a pseudogene. Mutations in this gene cause autosomal recessive non-syndromic deafness. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
?
Variant 15-43611297-A-AG is Pathogenic according to our data. Variant chr15-43611297-A-AG is described in ClinVar as [Pathogenic]. Clinvar id is 4343.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STRC | NM_153700.2 | c.3156_3157insC | p.Cys1053LeufsTer20 | frameshift_variant | 13/29 | ENST00000450892.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRC | ENST00000450892.7 | c.3156_3157insC | p.Cys1053LeufsTer20 | frameshift_variant | 13/29 | 5 | NM_153700.2 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 12
GnomAD3 genomes
?
Cov.:
12
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000406 AC: 2AN: 492756Hom.: 0 Cov.: 5 AF XY: 0.00000768 AC XY: 2AN XY: 260290
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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2
AN:
492756
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5
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2
AN XY:
260290
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 12
GnomAD4 genome
?
Cov.:
12
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 16 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2001 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at