5-83553500-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004385.5(VCAN):c.9630C>T(p.His3210His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00939 in 1,614,008 control chromosomes in the GnomAD database, including 1,265 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004385.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCAN | NM_004385.5 | c.9630C>T | p.His3210His | synonymous_variant | Exon 11 of 15 | ENST00000265077.8 | NP_004376.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0494 AC: 7509AN: 152112Hom.: 646 Cov.: 33
GnomAD3 exomes AF: 0.0133 AC: 3330AN: 250994Hom.: 278 AF XY: 0.00947 AC XY: 1285AN XY: 135666
GnomAD4 exome AF: 0.00521 AC: 7621AN: 1461778Hom.: 618 Cov.: 32 AF XY: 0.00440 AC XY: 3203AN XY: 727196
GnomAD4 genome AF: 0.0495 AC: 7530AN: 152230Hom.: 647 Cov.: 33 AF XY: 0.0476 AC XY: 3546AN XY: 74430
ClinVar
Submissions by phenotype
Wagner syndrome Benign:2
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not provided Benign:2
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not specified Benign:1
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Vitreoretinopathy Benign:1
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