rs16900532
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004385.5(VCAN):c.9033C>A(p.Asn3011Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00896 in 1,610,478 control chromosomes in the GnomAD database, including 1,147 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N3011D) has been classified as Uncertain significance.
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 | UniProt |
---|---|---|---|---|---|---|---|
VCAN | NM_004385.5 | c.9033C>A | p.Asn3011Lys | missense_variant | 8/15 | ENST00000265077.8 | |
VCAN-AS1 | NR_136215.1 | n.285-7863G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCAN | ENST00000265077.8 | c.9033C>A | p.Asn3011Lys | missense_variant | 8/15 | 1 | NM_004385.5 | ||
VCAN-AS1 | ENST00000513899.1 | n.229-335G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0466 AC: 7088AN: 152064Hom.: 572 Cov.: 32
GnomAD3 exomes AF: 0.0128 AC: 3194AN: 249700Hom.: 249 AF XY: 0.00909 AC XY: 1227AN XY: 134946
GnomAD4 exome AF: 0.00503 AC: 7329AN: 1458296Hom.: 574 Cov.: 34 AF XY: 0.00428 AC XY: 3102AN XY: 724860
GnomAD4 genome ? AF: 0.0467 AC: 7104AN: 152182Hom.: 573 Cov.: 32 AF XY: 0.0446 AC XY: 3315AN XY: 74408
ClinVar
Submissions by phenotype
Wagner syndrome Benign:2
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 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 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