chr19-54040977-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198481.4(VSTM1):c.695C>T(p.Ala232Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,609,608 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A232T) has been classified as Uncertain significance.
Frequency
Consequence
NM_198481.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.695C>T | p.Ala232Val | missense_variant | 9/9 | ENST00000338372.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VSTM1 | ENST00000338372.7 | c.695C>T | p.Ala232Val | missense_variant | 9/9 | 1 | NM_198481.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152044Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247146Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133834
GnomAD4 exome AF: 0.0000364 AC: 53AN: 1457564Hom.: 0 Cov.: 34 AF XY: 0.0000345 AC XY: 25AN XY: 725140
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152044Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74244
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2023 | The c.695C>T (p.A232V) alteration is located in exon 9 (coding exon 9) of the VSTM1 gene. This alteration results from a C to T substitution at nucleotide position 695, causing the alanine (A) at amino acid position 232 to be replaced by a valine (V). 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