chrX-129540456-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4BP6_Moderate
The NM_000276.4(OCRL):c.17C>G(p.Pro6Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,016,230 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P6L) has been classified as Likely benign.
Frequency
Consequence
NM_000276.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OCRL | NM_000276.4 | c.17C>G | p.Pro6Arg | missense_variant | 1/24 | ENST00000371113.9 | |
OCRL | NM_001318784.2 | c.17C>G | p.Pro6Arg | missense_variant | 1/24 | ||
OCRL | NM_001587.4 | c.17C>G | p.Pro6Arg | missense_variant | 1/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OCRL | ENST00000371113.9 | c.17C>G | p.Pro6Arg | missense_variant | 1/24 | 1 | NM_000276.4 | P1 | |
OCRL | ENST00000357121.5 | c.17C>G | p.Pro6Arg | missense_variant | 1/23 | 1 | |||
OCRL | ENST00000691455.1 | c.17C>G | p.Pro6Arg | missense_variant, NMD_transcript_variant | 1/18 | ||||
OCRL | ENST00000486673.1 | n.91+517C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 20
GnomAD3 exomes AF: 0.0000105 AC: 1AN: 95693Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 35065
GnomAD4 exome AF: 0.0000138 AC: 14AN: 1016230Hom.: 0 Cov.: 31 AF XY: 0.0000153 AC XY: 5AN XY: 326540
GnomAD4 genome ? Cov.: 20
ClinVar
Submissions by phenotype
Lowe syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at