rs1244308550
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_000393.5(COL5A2):c.2308G>T(p.Ala770Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,458,208 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A770A) 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A2 | NM_000393.5 | c.2308G>T | p.Ala770Ser | missense_variant | 34/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.2170G>T | p.Ala724Ser | missense_variant | 37/57 | ||
COL5A2 | XM_047443251.1 | c.2170G>T | p.Ala724Ser | missense_variant | 39/59 | ||
COL5A2 | XM_047443252.1 | c.2170G>T | p.Ala724Ser | missense_variant | 38/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.2308G>T | p.Ala770Ser | missense_variant | 34/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.1147G>T | p.Ala383Ser | missense_variant | 27/47 | 5 | |||
COL5A2 | ENST00000470524.2 | n.414G>T | non_coding_transcript_exon_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251104Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135730
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1458208Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 725542
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Connective tissue disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Human Genetics, Inc, Center for Human Genetics, Inc | Nov 01, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at