X-129539986-TA-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The ENST00000486673.1(OCRL):n.91+48delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00452 in 109,322 control chromosomes in the GnomAD database, including 2 homozygotes. There are 133 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0045 ( 2 hom., 133 hem., cov: 21)
Exomes 𝑓: 0.0028 ( 0 hom. 0 hem. )
Consequence
OCRL
ENST00000486673.1 intron
ENST00000486673.1 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.813
Genes affected
OCRL (HGNC:8108): (OCRL inositol polyphosphate-5-phosphatase) This gene encodes an inositol polyphosphate 5-phosphatase. This protein is involved in regulating membrane trafficking and is located in numerous subcellular locations including the trans-Golgi network, clathrin-coated vesicles and, endosomes and the plasma membrane. This protein may also play a role in primary cilium formation. Mutations in this gene cause oculocerebrorenal syndrome of Lowe and also Dent disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant X-129539986-TA-T is Benign according to our data. Variant chrX-129539986-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 1205397.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00452 (493/108967) while in subpopulation AFR AF= 0.0148 (442/29899). AF 95% confidence interval is 0.0136. There are 2 homozygotes in gnomad4. There are 133 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OCRL | ENST00000486673.1 | n.91+48delA | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00452 AC: 492AN: 108966Hom.: 2 Cov.: 21 AF XY: 0.00419 AC XY: 132AN XY: 31498
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GnomAD4 exome AF: 0.00282 AC: 1AN: 355Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 77
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GnomAD4 genome AF: 0.00452 AC: 493AN: 108967Hom.: 2 Cov.: 21 AF XY: 0.00422 AC XY: 133AN XY: 31515
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2020 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at