rs12086448
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_020335.3(VANGL2):āc.1137A>Gā(p.Lys379=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 1,613,826 control chromosomes in the GnomAD database, including 231,884 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.58 ( 26727 hom., cov: 31)
Exomes š: 0.53 ( 205157 hom. )
Consequence
VANGL2
NM_020335.3 synonymous
NM_020335.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.12
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 1-160424115-A-G is Benign according to our data. Variant chr1-160424115-A-G is described in ClinVar as [Benign]. Clinvar id is 1684206.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.12 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VANGL2 | NM_020335.3 | c.1137A>G | p.Lys379= | synonymous_variant | 7/8 | ENST00000368061.3 | NP_065068.1 | |
VANGL2 | XM_005245357.2 | c.1137A>G | p.Lys379= | synonymous_variant | 8/9 | XP_005245414.1 | ||
VANGL2 | XM_011509804.2 | c.1137A>G | p.Lys379= | synonymous_variant | 7/8 | XP_011508106.1 | ||
VANGL2 | XM_047426020.1 | c.1137A>G | p.Lys379= | synonymous_variant | 7/8 | XP_047281976.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VANGL2 | ENST00000368061.3 | c.1137A>G | p.Lys379= | synonymous_variant | 7/8 | 2 | NM_020335.3 | ENSP00000357040 | P1 | |
VANGL2 | ENST00000696602.1 | c.1281A>G | p.Lys427= | synonymous_variant | 7/8 | ENSP00000512747 | ||||
VANGL2 | ENST00000483408.1 | n.317A>G | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.579 AC: 88005AN: 151872Hom.: 26713 Cov.: 31
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GnomAD3 exomes AF: 0.511 AC: 128496AN: 251378Hom.: 34050 AF XY: 0.516 AC XY: 70085AN XY: 135862
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GnomAD4 exome AF: 0.527 AC: 769714AN: 1461836Hom.: 205157 Cov.: 82 AF XY: 0.528 AC XY: 383723AN XY: 727214
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GnomAD4 genome AF: 0.579 AC: 88064AN: 151990Hom.: 26727 Cov.: 31 AF XY: 0.576 AC XY: 42778AN XY: 74272
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Neural tube defect Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at