chrX-129540745-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000276.4(OCRL):c.41C>T(p.Thr14Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00689 in 1,205,712 control chromosomes in the GnomAD database, including 23 homozygotes. There are 2,616 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000276.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OCRL | NM_000276.4 | c.41C>T | p.Thr14Ile | missense_variant, splice_region_variant | Exon 2 of 24 | ENST00000371113.9 | NP_000267.2 | |
OCRL | NM_001318784.2 | c.44C>T | p.Thr15Ile | missense_variant | Exon 2 of 24 | NP_001305713.1 | ||
OCRL | NM_001587.4 | c.41C>T | p.Thr14Ile | missense_variant, splice_region_variant | Exon 2 of 23 | NP_001578.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OCRL | ENST00000371113.9 | c.41C>T | p.Thr14Ile | missense_variant, splice_region_variant | Exon 2 of 24 | 1 | NM_000276.4 | ENSP00000360154.4 | ||
OCRL | ENST00000357121.5 | c.41C>T | p.Thr14Ile | missense_variant, splice_region_variant | Exon 2 of 23 | 1 | ENSP00000349635.5 |
Frequencies
GnomAD3 genomes AF: 0.00482 AC: 534AN: 110771Hom.: 2 Cov.: 22 AF XY: 0.00449 AC XY: 148AN XY: 32975
GnomAD3 exomes AF: 0.00565 AC: 1036AN: 183264Hom.: 3 AF XY: 0.00612 AC XY: 415AN XY: 67778
GnomAD4 exome AF: 0.00710 AC: 7775AN: 1094892Hom.: 21 Cov.: 30 AF XY: 0.00685 AC XY: 2468AN XY: 360456
GnomAD4 genome AF: 0.00482 AC: 534AN: 110820Hom.: 2 Cov.: 22 AF XY: 0.00448 AC XY: 148AN XY: 33034
ClinVar
Submissions by phenotype
not provided Benign:6
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not specified Benign:4
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Lowe syndrome Benign:1
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Nephrolithiasis/nephrocalcinosis Benign:1
This alteration is classified as 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