rs751819198
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_000393.5(COL5A2):c.750G>T(p.Pro250=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,458,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P250P) has been classified as Likely benign.
Frequency
Consequence
NM_000393.5 synonymous
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.750G>T | p.Pro250= | synonymous_variant | 11/54 | ENST00000374866.9 | |
COL5A2 | XM_011510573.4 | c.612G>T | p.Pro204= | synonymous_variant | 14/57 | ||
COL5A2 | XM_047443251.1 | c.612G>T | p.Pro204= | synonymous_variant | 16/59 | ||
COL5A2 | XM_047443252.1 | c.612G>T | p.Pro204= | synonymous_variant | 15/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A2 | ENST00000374866.9 | c.750G>T | p.Pro250= | synonymous_variant | 11/54 | 1 | NM_000393.5 | P1 | |
COL5A2 | ENST00000618828.1 | c.120G>T | p.Pro40= | synonymous_variant | 11/47 | 5 | |||
COL5A2 | ENST00000649966.1 | c.612G>T | p.Pro204= | synonymous_variant | 11/11 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245984Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132674
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458088Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725050
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at