chr1-160415821-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_020335.3(VANGL2):c.-17C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000193 in 1,610,408 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 0 hom. )
Consequence
VANGL2
NM_020335.3 5_prime_UTR
NM_020335.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.45
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 -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 1-160415821-C-T is Benign according to our data. Variant chr1-160415821-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3388087.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 28 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VANGL2 | ENST00000368061 | c.-17C>T | 5_prime_UTR_variant | Exon 2 of 8 | 2 | NM_020335.3 | ENSP00000357040.2 | |||
VANGL2 | ENST00000696602.1 | c.128C>T | p.Ala43Val | missense_variant | Exon 2 of 8 | ENSP00000512747.1 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152230Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000196 AC: 47AN: 239662Hom.: 0 AF XY: 0.000169 AC XY: 22AN XY: 130022
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GnomAD4 exome AF: 0.000194 AC: 283AN: 1458178Hom.: 0 Cov.: 31 AF XY: 0.000201 AC XY: 146AN XY: 725008
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GnomAD4 genome AF: 0.000184 AC: 28AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74360
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
VANGL2: BS2 -
Computational scores
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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