chr15-43613218-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_153700.2(STRC):c.2494C>T(p.Arg832Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_153700.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 47476Hom.: 0 Cov.: 6 FAILED QC
GnomAD3 exomes AF: 0.0000403 AC: 2AN: 49592Hom.: 0 AF XY: 0.0000398 AC XY: 1AN XY: 25114
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000449 AC: 12AN: 267192Hom.: 0 Cov.: 4 AF XY: 0.0000413 AC XY: 6AN XY: 145166
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000421 AC: 2AN: 47476Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0AN XY: 22156
ClinVar
Submissions by phenotype
not provided Uncertain:3
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Reported in a patient with bilateral sensorineural hearing loss who also harbored a gene conversion event involving the STRC gene on the opposite allele (in trans) in the published literature (PMID: 36086952); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 36086952) -
The p.Arg832Trp variant in STRC has been identified by our laboratory in two individuals with hearing loss who also had a STRC/CATSPER2 deletion. This variant has been identified in 0.0001% (1/10124) Latino/Admixed American chromosomes and 0.006% (1/1742) other chromosomes by gnomAD (http://gnomad.broadinstitute.org); however, these frequency estimates may not be reliable due to low coverage of this region. Computational prediction tools and conservation analyses suggest that the Arg832Trp variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM3_Strong, PP3. -
Inborn genetic diseases Uncertain:1
The c.2494C>T (p.R832W) alteration is located in exon 8 (coding exon 8) of the STRC gene. This alteration results from a C to T substitution at nucleotide position 2494, causing the arginine (R) at amino acid position 832 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at