chr19-54051441-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198481.4(VSTM1):āc.363C>Gā(p.His121Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000277 in 1,441,480 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 (ā ).
Frequency
Consequence
NM_198481.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VSTM1 | NM_198481.4 | c.363C>G | p.His121Gln | missense_variant | 4/9 | ENST00000338372.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VSTM1 | ENST00000338372.7 | c.363C>G | p.His121Gln | missense_variant | 4/9 | 1 | NM_198481.4 | P2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000435 AC: 1AN: 230046Hom.: 0 AF XY: 0.00000798 AC XY: 1AN XY: 125330
GnomAD4 exome AF: 0.00000277 AC: 4AN: 1441480Hom.: 0 Cov.: 30 AF XY: 0.00000279 AC XY: 2AN XY: 717300
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.363C>G (p.H121Q) alteration is located in exon 4 (coding exon 4) of the VSTM1 gene. This alteration results from a C to G substitution at nucleotide position 363, causing the histidine (H) at amino acid position 121 to be replaced by a glutamine (Q). 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