Variant chrX-129540176-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The variant allele was found at a frequency of 0.0593 in 406,477 control chromosomes in the GnomAD database, including 1,525 homozygotes. There are 8,082 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.070 ( 443 hom., 2381 hem., cov: 22)

Exomes 𝑓: 0.055 ( 1082 hom. 5701 hem. )

Consequence

intergenic_region

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.471

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant X-129540176-C-T is Benign according to our data. Variant chrX-129540176-C-T is described in ClinVar as [Benign]. Clinvar id is 1259336.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.129540176C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OCRL	ENST00000486673.1 linkuse as main transcript	n.91+237C>T		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0703

AC:

7862

AN:

111861

Hom.:

444

Cov.:

AF XY:

0.0697

AC XY:

2373

AN XY:

34069

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0818

Gnomad ASJ

AF:

0.0207

Gnomad EAS

AF:

0.333

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.0147

Gnomad MID

AF:

0.0216

Gnomad NFE

AF:

0.0118

Gnomad OTH

AF:

0.0664

GnomAD4 exome

AF:

0.0551

AC:

16224

AN:

294579

Hom.:

1082

AF XY:

0.0601

AC XY:

5701

AN XY:

94875

show subpopulations

Gnomad4 AFR exome

AF:

0.153

Gnomad4 AMR exome

AF:

0.0959

Gnomad4 ASJ exome

AF:

0.0202

Gnomad4 EAS exome

AF:

0.322

Gnomad4 SAS exome

AF:

0.134

Gnomad4 FIN exome

AF:

0.0144

Gnomad4 NFE exome

AF:

0.0121

Gnomad4 OTH exome

AF:

0.0555

GnomAD4 genome

AF:

0.0703

AC:

7865

AN:

111898

Hom.:

443

Cov.:

AF XY:

0.0698

AC XY:

2381

AN XY:

34116

show subpopulations

Gnomad4 AFR

AF:

0.149

Gnomad4 AMR

AF:

0.0815

Gnomad4 ASJ

AF:

0.0207

Gnomad4 EAS

AF:

0.334

Gnomad4 SAS

AF:

0.137

Gnomad4 FIN

AF:

0.0147

Gnomad4 NFE

AF:

0.0118

Gnomad4 OTH

AF:

0.0663

Alfa

AF:

0.0442

Hom.:

212

Bravo

AF:

0.0849

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 27, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.94

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