2-189051396-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP2PP3
The NM_000393.5(COL5A2):c.2855G>T(p.Arg952Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,788 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R952C) has been classified as Likely benign.
Frequency
Consequence
NM_000393.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.2855G>T | p.Arg952Leu | missense_variant | 42/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.2717G>T | p.Arg906Leu | missense_variant | 45/57 | ||
COL5A2 | XM_047443251.1 | c.2717G>T | p.Arg906Leu | missense_variant | 47/59 | ||
COL5A2 | XM_047443252.1 | c.2717G>T | p.Arg906Leu | missense_variant | 46/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.2855G>T | p.Arg952Leu | missense_variant | 42/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.1694G>T | p.Arg565Leu | missense_variant | 35/47 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461788Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727188
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at