6-30923211-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_020442.6(VARS2):c.2293G>A(p.Val765Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00264 in 1,612,664 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_020442.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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VARS2 | NM_020442.6 | c.2293G>A | p.Val765Met | missense_variant | Exon 24 of 30 | ENST00000676266.1 | NP_065175.4 | |
VARS2 | NM_001167734.2 | c.2383G>A | p.Val795Met | missense_variant | Exon 24 of 30 | NP_001161206.1 | ||
VARS2 | NM_001167733.3 | c.1873G>A | p.Val625Met | missense_variant | Exon 23 of 29 | NP_001161205.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00258 AC: 393AN: 152222Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00275 AC: 677AN: 246580Hom.: 0 AF XY: 0.00253 AC XY: 340AN XY: 134414
GnomAD4 exome AF: 0.00264 AC: 3860AN: 1460324Hom.: 8 Cov.: 33 AF XY: 0.00261 AC XY: 1899AN XY: 726400
GnomAD4 genome AF: 0.00258 AC: 393AN: 152340Hom.: 2 Cov.: 33 AF XY: 0.00260 AC XY: 194AN XY: 74504
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:4
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VARS2: PM2, BP4 -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at