rs753516492
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080607.3(VSTM2L):c.316G>A(p.Ala106Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,459,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A106S) has been classified as Uncertain significance.
Frequency
Consequence
NM_080607.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VSTM2L | ENST00000373461.9 | c.316G>A | p.Ala106Thr | missense_variant | Exon 3 of 4 | 1 | NM_080607.3 | ENSP00000362560.4 | ||
VSTM2L | ENST00000448944.1 | c.291+1759G>A | intron_variant | Intron 2 of 2 | 3 | ENSP00000406537.1 | ||||
VSTM2L | ENST00000373459.4 | c.122-10418G>A | intron_variant | Intron 1 of 1 | 3 | ENSP00000362558.4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251240 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459004Hom.: 0 Cov.: 34 AF XY: 0.00000276 AC XY: 2AN XY: 725850 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at