rs13894
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_133491.5(SAT2):c.376C>T(p.Arg126Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0734 in 1,613,918 control chromosomes in the GnomAD database, including 4,557 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_133491.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAT2 | NM_133491.5 | c.376C>T | p.Arg126Cys | missense_variant | 6/6 | ENST00000269298.10 | NP_597998.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAT2 | ENST00000269298.10 | c.376C>T | p.Arg126Cys | missense_variant | 6/6 | 1 | NM_133491.5 | ENSP00000269298 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0713 AC: 10856AN: 152158Hom.: 384 Cov.: 31
GnomAD3 exomes AF: 0.0695 AC: 17433AN: 250946Hom.: 694 AF XY: 0.0717 AC XY: 9725AN XY: 135656
GnomAD4 exome AF: 0.0736 AC: 107596AN: 1461642Hom.: 4170 Cov.: 32 AF XY: 0.0749 AC XY: 54427AN XY: 727120
GnomAD4 genome AF: 0.0713 AC: 10863AN: 152276Hom.: 387 Cov.: 31 AF XY: 0.0702 AC XY: 5224AN XY: 74448
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at