rs568686157
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015719.4(COL5A3):c.5089C>T(p.Arg1697Trp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_015719.4 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A3 | NM_015719.4 | c.5089C>T | p.Arg1697Trp | missense_variant, splice_region_variant | Exon 66 of 67 | ENST00000264828.4 | NP_056534.2 | |
COL5A3 | XM_011528042.3 | c.5086C>T | p.Arg1696Trp | missense_variant, splice_region_variant | Exon 66 of 67 | XP_011526344.1 | ||
COL5A3 | XM_017026849.2 | c.2752C>T | p.Arg918Trp | missense_variant, splice_region_variant | Exon 39 of 40 | XP_016882338.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 250748Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135580
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1461598Hom.: 0 Cov.: 40 AF XY: 0.0000330 AC XY: 24AN XY: 727122
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74434
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at