chr1-160421119-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_020335.3(VANGL2):c.1005C>T(p.Asp335=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00105 in 1,614,056 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0056 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00057 ( 7 hom. )
Consequence
VANGL2
NM_020335.3 synonymous
NM_020335.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.83
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
Variant 1-160421119-C-T is Benign according to our data. Variant chr1-160421119-C-T is described in ClinVar as [Benign]. Clinvar id is 720022.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0056 (853/152206) while in subpopulation AFR AF= 0.019 (789/41524). AF 95% confidence interval is 0.0179. There are 5 homozygotes in gnomad4. There are 430 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 851 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VANGL2 | NM_020335.3 | c.1005C>T | p.Asp335= | synonymous_variant | 6/8 | ENST00000368061.3 | |
VANGL2 | XM_005245357.2 | c.1005C>T | p.Asp335= | synonymous_variant | 7/9 | ||
VANGL2 | XM_011509804.2 | c.1005C>T | p.Asp335= | synonymous_variant | 6/8 | ||
VANGL2 | XM_047426020.1 | c.1005C>T | p.Asp335= | synonymous_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VANGL2 | ENST00000368061.3 | c.1005C>T | p.Asp335= | synonymous_variant | 6/8 | 2 | NM_020335.3 | P1 | |
VANGL2 | ENST00000696602.1 | c.1149C>T | p.Asp383= | synonymous_variant | 6/8 | ||||
VANGL2 | ENST00000483408.1 | n.185C>T | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00560 AC: 851AN: 152090Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.00135 AC: 339AN: 251360Hom.: 2 AF XY: 0.00102 AC XY: 139AN XY: 135868
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GnomAD4 exome AF: 0.000573 AC: 838AN: 1461850Hom.: 7 Cov.: 32 AF XY: 0.000521 AC XY: 379AN XY: 727228
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at