2-189064615-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_000393.5(COL5A2):c.1658C>T(p.Pro553Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,724 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P553R) has been classified as Uncertain significance.
Frequency
Consequence
NM_000393.5 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.1658C>T | p.Pro553Leu | missense_variant | 25/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.1520C>T | p.Pro507Leu | missense_variant | 28/57 | ||
COL5A2 | XM_047443251.1 | c.1520C>T | p.Pro507Leu | missense_variant | 30/59 | ||
COL5A2 | XM_047443252.1 | c.1520C>T | p.Pro507Leu | missense_variant | 29/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.1658C>T | p.Pro553Leu | missense_variant | 25/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.497C>T | p.Pro166Leu | missense_variant | 18/47 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151818Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251248Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135826
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461788Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727200
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151936Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74236
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at