5-83537619-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004385.5(VCAN):c.4616C>A(p.Pro1539His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1539L) has been classified as Uncertain significance.
Frequency
Consequence
NM_004385.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VCAN | NM_004385.5 | c.4616C>A | p.Pro1539His | missense_variant | 8/15 | ENST00000265077.8 | |
VCAN-AS1 | NR_136215.1 | n.285-3446G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCAN | ENST00000265077.8 | c.4616C>A | p.Pro1539His | missense_variant | 8/15 | 1 | NM_004385.5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 77
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at