chr6-30914912-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020442.6(VARS2):c.76C>T(p.His26Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 1,613,038 control chromosomes in the GnomAD database, including 2,010 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 Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_020442.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VARS2 | NM_020442.6 | c.76C>T | p.His26Tyr | missense_variant | 2/30 | ENST00000676266.1 | |
VARS2 | NM_001167734.2 | c.166C>T | p.His56Tyr | missense_variant | 2/30 | ||
VARS2 | NM_001167733.3 | c.-219-244C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VARS2 | ENST00000676266.1 | c.76C>T | p.His26Tyr | missense_variant | 2/30 | NM_020442.6 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0646 AC: 9828AN: 152150Hom.: 499 Cov.: 32
GnomAD3 exomes AF: 0.0507 AC: 12514AN: 246594Hom.: 502 AF XY: 0.0467 AC XY: 6274AN XY: 134420
GnomAD4 exome AF: 0.0365 AC: 53338AN: 1460770Hom.: 1509 Cov.: 62 AF XY: 0.0362 AC XY: 26328AN XY: 726704
GnomAD4 genome AF: 0.0646 AC: 9841AN: 152268Hom.: 501 Cov.: 32 AF XY: 0.0638 AC XY: 4750AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 29, 2016 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 17, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at