rs766925699
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP3_Moderate
The NM_000393.5(COL5A2):c.173C>T(p.Pro58Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,856 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P58H) has been classified as Uncertain significance.
Frequency
Consequence
NM_000393.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.173C>T | p.Pro58Leu | missense_variant | 2/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.35C>T | p.Pro12Leu | missense_variant | 5/57 | ||
COL5A2 | XM_047443251.1 | c.35C>T | p.Pro12Leu | missense_variant | 7/59 | ||
COL5A2 | XM_047443252.1 | c.35C>T | p.Pro12Leu | missense_variant | 6/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.173C>T | p.Pro58Leu | missense_variant | 2/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000649966.1 | c.35C>T | p.Pro12Leu | missense_variant | 2/11 | ||||
COL5A2 | ENST00000618828.1 | c.-458C>T | 5_prime_UTR_variant | 2/47 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251380Hom.: 1 AF XY: 0.0000147 AC XY: 2AN XY: 135846
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461856Hom.: 1 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 727228
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at