chr10-49107762-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000332853.9(VSTM4):c.289C>T(p.Arg97Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,614,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000332853.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VSTM4 | NM_001031746.5 | c.289C>T | p.Arg97Trp | 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.289C>T | p.Arg97Trp | missense_variant | 2/8 | 1 | NM_001031746.5 | ENSP00000331062 | P1 | |
VSTM4 | ENST00000298454.3 | c.289C>T | p.Arg97Trp | missense_variant | 2/3 | 2 | ENSP00000298454 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251406Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135882
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461858Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727230
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2024 | The c.289C>T (p.R97W) alteration is located in exon 2 (coding exon 2) of the VSTM4 gene. This alteration results from a C to T substitution at nucleotide position 289, causing the arginine (R) at amino acid position 97 to be replaced by a tryptophan (W). 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