rs184909019
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_Very_StrongBP7BS2_Supporting
The NM_153700.2(STRC):c.4845C>T(p.Ser1615=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,613,434 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_153700.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STRC | NM_153700.2 | c.4845C>T | p.Ser1615= | splice_region_variant, synonymous_variant | 26/29 | ENST00000450892.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRC | ENST00000450892.7 | c.4845C>T | p.Ser1615= | splice_region_variant, synonymous_variant | 26/29 | 5 | NM_153700.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 151886Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.000247 AC: 62AN: 251194Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135828
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461434Hom.: 3 Cov.: 34 AF XY: 0.0000591 AC XY: 43AN XY: 727020
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152000Hom.: 0 Cov.: 28 AF XY: 0.000121 AC XY: 9AN XY: 74304
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 25, 2017 | p.Ser1615Ser in exon 26 of STRC: This variant is not expected to have clinical s ignificance because it has been identified in 0.38% (71/18854) of East Asian chr omosomes including 1 homozygote by the Genome Aggregation Database (gnomAD, http ://gnomad.broadinstitute.org; dbSNP rs184909019). This variant does not alter a n amino acid residue; however, it is located in the first base of the exon. It is not predicted to impact splicing. - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 29, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Autosomal recessive nonsyndromic hearing loss 16 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at