Genetic Variant ENST00000486673.1:n.91+38_91+39delAT (chrX-129539976-AAT-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000486673.1(OCRL):n.91+38_91+39delAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 101,405 control chromosomes in the GnomAD database, including 445 homozygotes. There are 1,351 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.060 ( 445 hom., 1350 hem., cov: 16)

Exomes 𝑓: 0.13 ( 0 hom. 1 hem. )

Consequence

OCRL
ENST00000486673.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0610

Variant links:

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]

OCRL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant X-129539976-AAT-A is Benign according to our data. Variant chrX-129539976-AAT-A is described in ClinVar as [Benign]. Clinvar id is 1289850.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OCRL	ENST00000486673.1 link	n.91+38_91+39delAT		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes

AF:

0.0600

AC:

6080

AN:

101401

Hom.:

445

Cov.:

AF XY:

0.0509

AC XY:

1346

AN XY:

26449

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0325

Gnomad ASJ

AF:

0.00200

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000450

Gnomad FIN

AF:

0.00793

Gnomad MID

AF:

0.0135

Gnomad NFE

AF:

0.00131

Gnomad OTH

AF:

0.0549

GnomAD4 exome

AF:

0.125

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.00

GnomAD4 genome

AF:

0.0600

AC:

6085

AN:

101397

Hom.:

445

Cov.:

AF XY:

0.0510

AC XY:

1350

AN XY:

26459

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.0325

Gnomad4 ASJ

AF:

0.00200

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000453

Gnomad4 FIN

AF:

0.00793

Gnomad4 NFE

AF:

0.00131

Gnomad4 OTH

AF:

0.0543

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Nov 06, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over