rs372897632
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_000393.5(COL5A2):c.3913G>T(p.Ala1305Ser) 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 1,461,638 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign 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. A1305T) 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.3913G>T | p.Ala1305Ser | missense_variant | 51/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.3775G>T | p.Ala1259Ser | missense_variant | 54/57 | ||
COL5A2 | XM_047443251.1 | c.3775G>T | p.Ala1259Ser | missense_variant | 56/59 | ||
COL5A2 | XM_047443252.1 | c.3775G>T | p.Ala1259Ser | missense_variant | 55/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.3913G>T | p.Ala1305Ser | missense_variant | 51/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.2752G>T | p.Ala918Ser | missense_variant | 44/47 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249994Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135240
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461638Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727144
GnomAD4 genome ? Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at