chr6-31779171-C-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS1
The NM_006295.3(VARS1):c.3522G>C(p.Gln1174His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000307 in 1,605,450 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006295.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VARS1 | NM_006295.3 | c.3522G>C | p.Gln1174His | missense_variant | 29/30 | ENST00000375663.8 | |
VARS1 | XM_005249362.3 | c.3525G>C | p.Gln1175His | missense_variant | 29/30 | ||
VARS1 | XM_047419296.1 | c.3525G>C | p.Gln1175His | missense_variant | 28/29 | ||
VARS1 | XM_047419297.1 | c.3522G>C | p.Gln1174His | missense_variant | 28/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VARS1 | ENST00000375663.8 | c.3522G>C | p.Gln1174His | missense_variant | 29/30 | 1 | NM_006295.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00150 AC: 228AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000423 AC: 95AN: 224664Hom.: 0 AF XY: 0.000258 AC XY: 32AN XY: 124204
GnomAD4 exome AF: 0.000182 AC: 265AN: 1453104Hom.: 4 Cov.: 32 AF XY: 0.000151 AC XY: 109AN XY: 722774
GnomAD4 genome ? AF: 0.00150 AC: 228AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.00157 AC XY: 117AN XY: 74500
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
VARS1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 17, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at