rs2074506
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020442.6(VARS2):c.2038G>A(p.Val680Met) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000685 in 1,459,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_020442.6 missense, splice_region
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VARS2 | NM_020442.6 | c.2038G>A | p.Val680Met | missense_variant, splice_region_variant | Exon 22 of 30 | ENST00000676266.1 | NP_065175.4 | |
VARS2 | NM_001167734.2 | c.2128G>A | p.Val710Met | missense_variant, splice_region_variant | Exon 22 of 30 | NP_001161206.1 | ||
VARS2 | NM_001167733.3 | c.1618G>A | p.Val540Met | missense_variant, splice_region_variant | Exon 21 of 29 | NP_001161205.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459802Hom.: 0 Cov.: 52 AF XY: 0.00000138 AC XY: 1AN XY: 726156
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.