chr2-189064615-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP2PP3BS2
The NM_000393.5(COL5A2):āc.1658C>Gā(p.Pro553Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,461,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P553H) 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.1658C>G | p.Pro553Arg | missense_variant | 25/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.1520C>G | p.Pro507Arg | missense_variant | 28/57 | ||
COL5A2 | XM_047443251.1 | c.1520C>G | p.Pro507Arg | missense_variant | 30/59 | ||
COL5A2 | XM_047443252.1 | c.1520C>G | p.Pro507Arg | missense_variant | 29/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.1658C>G | p.Pro553Arg | missense_variant | 25/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.497C>G | p.Pro166Arg | missense_variant | 18/47 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251248Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135826
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461788Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727200
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Connective tissue disorder Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Human Genetics, Inc, Center for Human Genetics, Inc | Nov 01, 2016 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 09, 2019 | Has not been previously published as pathogenic or benign to our knowledge; Reported in ClinVar as a variant of uncertain significance (ClinVar Variant ID# 547287; Landrum et al., 2016); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect - |
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 05, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at