1-160416081-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_020335.3(VANGL2):c.91C>T(p.Arg31Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000297 in 1,614,244 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_020335.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VANGL2 | ENST00000368061.3 | c.91C>T | p.Arg31Cys | missense_variant | Exon 3 of 8 | 2 | NM_020335.3 | ENSP00000357040.2 | ||
VANGL2 | ENST00000696602.1 | c.235C>T | p.Arg79Cys | missense_variant | Exon 3 of 8 | ENSP00000512747.1 |
Frequencies
GnomAD3 genomes AF: 0.000985 AC: 150AN: 152238Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000334 AC: 84AN: 251162Hom.: 0 AF XY: 0.000324 AC XY: 44AN XY: 135856
GnomAD4 exome AF: 0.000226 AC: 330AN: 1461888Hom.: 4 Cov.: 31 AF XY: 0.000209 AC XY: 152AN XY: 727246
GnomAD4 genome AF: 0.000985 AC: 150AN: 152356Hom.: 2 Cov.: 32 AF XY: 0.00106 AC XY: 79AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:2
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VANGL2-related disorder Benign:1
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