rs13088
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001031746.5(VSTM4):āc.203T>Cā(p.Phe68Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 1,613,938 control chromosomes in the GnomAD database, including 142,856 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict 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_001031746.5 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 |
---|---|---|---|---|---|---|---|---|
VSTM4 | NM_001031746.5 | c.203T>C | p.Phe68Ser | missense_variant | 2/8 | ENST00000332853.9 | NP_001026916.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VSTM4 | ENST00000332853.9 | c.203T>C | p.Phe68Ser | missense_variant | 2/8 | 1 | NM_001031746.5 | ENSP00000331062.3 | ||
VSTM4 | ENST00000298454.3 | c.203T>C | p.Phe68Ser | missense_variant | 2/3 | 2 | ENSP00000298454.3 |
Frequencies
GnomAD3 genomes AF: 0.485 AC: 73668AN: 151992Hom.: 19362 Cov.: 33
GnomAD3 exomes AF: 0.423 AC: 106238AN: 251230Hom.: 23899 AF XY: 0.420 AC XY: 57082AN XY: 135808
GnomAD4 exome AF: 0.405 AC: 592248AN: 1461826Hom.: 123466 Cov.: 90 AF XY: 0.407 AC XY: 295650AN XY: 727208
GnomAD4 genome AF: 0.485 AC: 73753AN: 152112Hom.: 19390 Cov.: 33 AF XY: 0.483 AC XY: 35923AN XY: 74354
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at