19-54041079-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198481.4(VSTM1):c.593C>T(p.Thr198Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 1,425,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198481.4 missense, splice_region
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.593C>T | p.Thr198Met | missense_variant, splice_region_variant | 9/9 | ENST00000338372.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VSTM1 | ENST00000338372.7 | c.593C>T | p.Thr198Met | missense_variant, splice_region_variant | 9/9 | 1 | NM_198481.4 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.0000191 AC: 4AN: 209746Hom.: 0 AF XY: 0.0000174 AC XY: 2AN XY: 114780
GnomAD4 exome AF: 0.0000182 AC: 26AN: 1425326Hom.: 0 Cov.: 34 AF XY: 0.0000155 AC XY: 11AN XY: 708654
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 17, 2023 | The c.593C>T (p.T198M) 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 593, causing the threonine (T) at amino acid position 198 to be replaced by a methionine (M). 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