rs758136981
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PP2PP3_ModerateBP6_ModerateBS2
The NM_000393.5(COL5A2):c.3880C>T(p.Arg1294Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000217 in 1,613,908 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1294H) has been classified as Likely benign.
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.3880C>T | p.Arg1294Cys | missense_variant | 51/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.3742C>T | p.Arg1248Cys | missense_variant | 54/57 | ||
COL5A2 | XM_047443251.1 | c.3742C>T | p.Arg1248Cys | missense_variant | 56/59 | ||
COL5A2 | XM_047443252.1 | c.3742C>T | p.Arg1248Cys | missense_variant | 55/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.3880C>T | p.Arg1294Cys | missense_variant | 51/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.2719C>T | p.Arg907Cys | missense_variant | 44/47 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250976Hom.: 1 AF XY: 0.0000590 AC XY: 8AN XY: 135690
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461834Hom.: 1 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727224
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74254
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at