chr10-114285997-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001272046.2(VWA2):c.1056G>A(p.Ala352=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00438 in 1,613,772 control chromosomes in the GnomAD database, including 251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.023 ( 117 hom., cov: 33)
Exomes 𝑓: 0.0025 ( 134 hom. )
Consequence
VWA2
NM_001272046.2 synonymous
NM_001272046.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.46
Genes affected
VWA2 (HGNC:24709): (von Willebrand factor A domain containing 2) This gene encodes a member of the von Willebrand factor A-like domain protein superfamily. The encoded protein is localized to the extracellular matrix and may serve as a structural component in basement membranes or in anchoring structures on scaffolds of collagen VII or fibrillin. This gene has been linked to type 1A diabetes and is a candidate serological marker for colon cancer. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
Variant 10-114285997-G-A is Benign according to our data. Variant chr10-114285997-G-A is described in ClinVar as [Benign]. Clinvar id is 769373.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.46 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0747 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWA2 | NM_001272046.2 | c.1056G>A | p.Ala352= | synonymous_variant | 11/14 | ENST00000392982.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWA2 | ENST00000392982.8 | c.1056G>A | p.Ala352= | synonymous_variant | 11/14 | 1 | NM_001272046.2 | P1 | |
VWA2 | ENST00000603594.2 | c.144G>A | p.Ala48= | synonymous_variant | 10/11 | 2 | |||
VWA2 | ENST00000298715.8 | n.1306G>A | non_coding_transcript_exon_variant | 11/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0226 AC: 3438AN: 152216Hom.: 117 Cov.: 33
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GnomAD3 exomes AF: 0.00589 AC: 1476AN: 250504Hom.: 42 AF XY: 0.00433 AC XY: 586AN XY: 135394
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GnomAD4 exome AF: 0.00248 AC: 3620AN: 1461438Hom.: 134 Cov.: 31 AF XY: 0.00214 AC XY: 1559AN XY: 726966
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GnomAD4 genome ? AF: 0.0226 AC: 3448AN: 152334Hom.: 117 Cov.: 33 AF XY: 0.0217 AC XY: 1620AN XY: 74494
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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 | Dec 20, 2018 | - - |
Computational 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