rs372244245
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_004385.5(VCAN):c.4007G>A(p.Arg1336Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,583,662 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_004385.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCAN | NM_004385.5 | c.4007G>A | p.Arg1336Gln | missense_variant | Exon 8 of 15 | ENST00000265077.8 | NP_004376.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 151990Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000109 AC: 25AN: 228784Hom.: 0 AF XY: 0.000122 AC XY: 15AN XY: 123432
GnomAD4 exome AF: 0.000109 AC: 156AN: 1431554Hom.: 1 Cov.: 29 AF XY: 0.000103 AC XY: 73AN XY: 709812
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74356
ClinVar
Submissions by phenotype
not provided Uncertain:2
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This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1336 of the VCAN protein (p.Arg1336Gln). This variant is present in population databases (rs372244245, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with VCAN-related conditions. ClinVar contains an entry for this variant (Variation ID: 1021566). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at