rs149646700
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_000276.4(OCRL):c.954C>T(p.Arg318=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000688 in 1,206,819 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 25 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000276.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OCRL | NM_000276.4 | c.954C>T | p.Arg318= | synonymous_variant | 11/24 | ENST00000371113.9 | |
OCRL | NM_001318784.2 | c.957C>T | p.Arg319= | synonymous_variant | 11/24 | ||
OCRL | NM_001587.4 | c.954C>T | p.Arg318= | synonymous_variant | 11/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OCRL | ENST00000371113.9 | c.954C>T | p.Arg318= | synonymous_variant | 11/24 | 1 | NM_000276.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000314 AC: 35AN: 111587Hom.: 0 Cov.: 22 AF XY: 0.000266 AC XY: 9AN XY: 33775
GnomAD3 exomes AF: 0.0000872 AC: 16AN: 183431Hom.: 0 AF XY: 0.0000589 AC XY: 4AN XY: 67887
GnomAD4 exome AF: 0.0000438 AC: 48AN: 1095232Hom.: 0 Cov.: 30 AF XY: 0.0000443 AC XY: 16AN XY: 360786
GnomAD4 genome ? AF: 0.000314 AC: 35AN: 111587Hom.: 0 Cov.: 22 AF XY: 0.000266 AC XY: 9AN XY: 33775
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 23, 2015 | - - |
Lowe syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 22, 2021 | - - |
Nephrolithiasis/nephrocalcinosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 18, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at