2-189048214-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_ModerateBP6_Moderate
The NM_000393.5(COL5A2):c.3196G>A(p.Glu1066Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,534 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.3196G>A | p.Glu1066Lys | missense_variant | 45/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.3058G>A | p.Glu1020Lys | missense_variant | 48/57 | ||
COL5A2 | XM_047443251.1 | c.3058G>A | p.Glu1020Lys | missense_variant | 50/59 | ||
COL5A2 | XM_047443252.1 | c.3058G>A | p.Glu1020Lys | missense_variant | 49/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.3196G>A | p.Glu1066Lys | missense_variant | 45/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.2035G>A | p.Glu679Lys | missense_variant | 38/47 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251416Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135896
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461534Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727096
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at