rs2287926
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004385.5(VCAN):c.1283G>A(p.Gly428Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,613,872 control chromosomes in the GnomAD database, including 16,434 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004385.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCAN | NM_004385.5 | c.1283G>A | p.Gly428Asp | missense_variant | 7/15 | ENST00000265077.8 | NP_004376.2 | |
VCAN | NM_001164098.2 | c.1283G>A | p.Gly428Asp | missense_variant | 7/14 | NP_001157570.1 | ||
VCAN | NM_001164097.2 | c.1042+7193G>A | intron_variant | NP_001157569.1 | ||||
VCAN | NM_001126336.3 | c.1042+7193G>A | intron_variant | NP_001119808.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VCAN | ENST00000265077.8 | c.1283G>A | p.Gly428Asp | missense_variant | 7/15 | 1 | NM_004385.5 | ENSP00000265077.3 |
Frequencies
GnomAD3 genomes AF: 0.169 AC: 25704AN: 151944Hom.: 2613 Cov.: 33
GnomAD3 exomes AF: 0.149 AC: 37335AN: 251100Hom.: 3209 AF XY: 0.150 AC XY: 20336AN XY: 135752
GnomAD4 exome AF: 0.130 AC: 190217AN: 1461810Hom.: 13821 Cov.: 33 AF XY: 0.132 AC XY: 96226AN XY: 727198
GnomAD4 genome AF: 0.169 AC: 25717AN: 152062Hom.: 2613 Cov.: 33 AF XY: 0.170 AC XY: 12612AN XY: 74320
ClinVar
Submissions by phenotype
Wagner syndrome Benign:5
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | Feb 04, 2014 | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 02, 2020 | This variant is associated with the following publications: (PMID: 25606449) - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Vitreoretinopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at