5-83483578-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004385.5(VCAN):c.60G>T(p.Ala20Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,460,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004385.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCAN | NM_004385.5 | c.60G>T | p.Ala20Ala | synonymous_variant | Exon 2 of 15 | ENST00000265077.8 | NP_004376.2 | |
VCAN | NM_001164097.2 | c.60G>T | p.Ala20Ala | synonymous_variant | Exon 2 of 14 | NP_001157569.1 | ||
VCAN | NM_001164098.2 | c.60G>T | p.Ala20Ala | synonymous_variant | Exon 2 of 14 | NP_001157570.1 | ||
VCAN | NM_001126336.3 | c.60G>T | p.Ala20Ala | synonymous_variant | Exon 2 of 13 | NP_001119808.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251158Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135760
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1460938Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726808
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at