Variant chrX-11254716-CAAA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1

The NM_013427.3(ARHGAP6):c.589-12_589-10delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 809,472 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00017 ( 0 hom., 0 hem., cov: 19)

Exomes 𝑓: 0.011 ( 0 hom. 0 hem. )

Consequence

ARHGAP6
NM_013427.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0850

Variant links:

Genes affected

ARHGAP6 (HGNC:676): (Rho GTPase activating protein 6) This gene encodes a member of the rhoGAP family of proteins which play a role in the regulation of actin polymerization at the plasma membrane during several cellular processes. This protein is thought to have two independent functions, one as a GTPase-activating protein with specificity for RhoA, and another as a cytoskeletal protein that promotes actin remodeling. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ARHGAP6 links:

ARHGAP6 (HGNC:):

ARHGAP6 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant X-11254716-CAAA-C is Benign according to our data. Variant chrX-11254716-CAAA-C is described in ClinVar as [Benign]. Clinvar id is 402392.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0108 (8331/774153) while in subpopulation AMR AF= 0.0285 (272/9534). AF 95% confidence interval is 0.0257. There are 0 homozygotes in gnomad4_exome. There are 0 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP6	NM_013427.3 linkuse as main transcript	c.589-12_589-10delTTT		intron_variant		ENST00000337414.9	NP_038286.2	O43182-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP6	ENST00000337414.9 linkuse as main transcript	c.589-12_589-10delTTT		intron_variant		1	NM_013427.3	ENSP00000338967.4		O43182-1

Frequencies

GnomAD3 genomes

AF:

0.000170

AC:

AN:

35319

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

5875

show subpopulations

Gnomad AFR

AF:

0.000216

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000304

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00272

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0613

AC:

920

AN:

15013

Hom.:

AF XY:

0.00

AC XY:

AN XY:

991

show subpopulations

Gnomad AFR exome

AF:

0.0571

Gnomad AMR exome

AF:

0.0685

Gnomad ASJ exome

AF:

0.0531

Gnomad EAS exome

AF:

0.0546

Gnomad SAS exome

AF:

0.0699

Gnomad FIN exome

AF:

0.00902

Gnomad NFE exome

AF:

0.0795

Gnomad OTH exome

AF:

0.0442

GnomAD4 exome

AF:

0.0108

AC:

8331

AN:

774153

Hom.:

AF XY:

0.00

AC XY:

AN XY:

217783

show subpopulations

Gnomad4 AFR exome

AF:

0.0146

Gnomad4 AMR exome

AF:

0.0285

Gnomad4 ASJ exome

AF:

0.0150

Gnomad4 EAS exome

AF:

0.0139

Gnomad4 SAS exome

AF:

0.0151

Gnomad4 FIN exome

AF:

0.0146

Gnomad4 NFE exome

AF:

0.00988

Gnomad4 OTH exome

AF:

0.0127

GnomAD4 genome

AF:

0.000170

AC:

AN:

35319

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

5875

show subpopulations

Gnomad4 AFR

AF:

0.000216

Gnomad4 AMR

AF:

0.000304

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00272

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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