rs17380141
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_020335.3(VANGL2):c.1401G>A(p.Pro467=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 1,613,824 control chromosomes in the GnomAD database, including 63,777 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.26 ( 5345 hom., cov: 31)
Exomes 𝑓: 0.28 ( 58432 hom. )
Consequence
VANGL2
NM_020335.3 synonymous
NM_020335.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.189
Genes affected
VANGL2 (HGNC:15511): (VANGL planar cell polarity protein 2) The protein encoded by this gene is a membrane protein involved in the regulation of planar cell polarity, especially in the stereociliary bundles of the cochlea. The encoded protein transmits directional signals to individual cells or groups of cells in epithelial sheets. This protein is also involved in the development of the neural plate. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP7
?
Synonymous conserved (PhyloP=-0.189 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VANGL2 | NM_020335.3 | c.1401G>A | p.Pro467= | synonymous_variant | 8/8 | ENST00000368061.3 | |
VANGL2 | XM_005245357.2 | c.1401G>A | p.Pro467= | synonymous_variant | 9/9 | ||
VANGL2 | XM_011509804.2 | c.1401G>A | p.Pro467= | synonymous_variant | 8/8 | ||
VANGL2 | XM_047426020.1 | c.1401G>A | p.Pro467= | synonymous_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VANGL2 | ENST00000368061.3 | c.1401G>A | p.Pro467= | synonymous_variant | 8/8 | 2 | NM_020335.3 | P1 | |
VANGL2 | ENST00000696602.1 | c.1545G>A | p.Pro515= | synonymous_variant | 8/8 |
Frequencies
GnomAD3 genomes ? AF: 0.258 AC: 39248AN: 151848Hom.: 5345 Cov.: 31
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GnomAD3 exomes AF: 0.253 AC: 63698AN: 251294Hom.: 8490 AF XY: 0.261 AC XY: 35414AN XY: 135812
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GnomAD4 exome AF: 0.280 AC: 408893AN: 1461858Hom.: 58432 Cov.: 52 AF XY: 0.280 AC XY: 203920AN XY: 727224
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GnomAD4 genome ? AF: 0.258 AC: 39266AN: 151966Hom.: 5345 Cov.: 31 AF XY: 0.256 AC XY: 19014AN XY: 74270
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at