rs956270311
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003098.3(SNTA1):c.129C>T(p.Ser43Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000486 in 1,379,870 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003098.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000727 AC: 11AN: 151298Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000691 AC: 5AN: 72404Hom.: 0 AF XY: 0.0000238 AC XY: 1AN XY: 41968
GnomAD4 exome AF: 0.0000456 AC: 56AN: 1228572Hom.: 1 Cov.: 31 AF XY: 0.0000381 AC XY: 23AN XY: 603434
GnomAD4 genome AF: 0.0000727 AC: 11AN: 151298Hom.: 0 Cov.: 31 AF XY: 0.0000812 AC XY: 6AN XY: 73874
ClinVar
Submissions by phenotype
not provided Benign:1
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Long QT syndrome Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at