chr19-54041038-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198481.4(VSTM1):c.634A>G(p.Ser212Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,607,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198481.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VSTM1 | NM_198481.4 | c.634A>G | p.Ser212Gly | missense_variant | 9/9 | ENST00000338372.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VSTM1 | ENST00000338372.7 | c.634A>G | p.Ser212Gly | missense_variant | 9/9 | 1 | NM_198481.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152074Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245434Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133080
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1455836Hom.: 0 Cov.: 34 AF XY: 0.00000414 AC XY: 3AN XY: 724388
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152074Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.634A>G (p.S212G) alteration is located in exon 9 (coding exon 9) of the VSTM1 gene. This alteration results from a A to G substitution at nucleotide position 634, causing the serine (S) at amino acid position 212 to be replaced by a glycine (G). 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