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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_013427.3(ARHGAP6):c.589-12_589-10dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0048 ( 0 hom., 9 hem., cov: 19)

Exomes 𝑓: 0.00029 ( 0 hom. 1 hem. )

Consequence

ARHGAP6
NM_013427.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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.

BS2

High Hemizygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes

AF:

0.00479

AC:

169

AN:

35278

Hom.:

Cov.:

AF XY:

0.00153

AC XY:

AN XY:

5870

show subpopulations

Gnomad AFR

AF:

0.0159

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000608

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00156

Gnomad FIN

AF:

0.000908

Gnomad MID

AF:

0.0147

Gnomad NFE

AF:

0.000823

Gnomad OTH

AF:

0.00438

GnomAD4 exome

AF:

0.000290

AC:

241

AN:

831868

Hom.:

Cov.:

AF XY:

0.00000415

AC XY:

AN XY:

241248

show subpopulations

Gnomad4 AFR exome

AF:

0.00239

Gnomad4 AMR exome

AF:

0.000967

Gnomad4 ASJ exome

AF:

0.000270

Gnomad4 EAS exome

AF:

0.0000915

Gnomad4 SAS exome

AF:

0.000927

Gnomad4 FIN exome

AF:

0.000227

Gnomad4 NFE exome

AF:

0.000204

Gnomad4 OTH exome

AF:

0.000496

GnomAD4 genome

AF:

0.00482

AC:

170

AN:

35274

Hom.:

Cov.:

AF XY:

0.00153

AC XY:

AN XY:

5872

show subpopulations

Gnomad4 AFR

AF:

0.0160

Gnomad4 AMR

AF:

0.000608

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00158

Gnomad4 FIN

AF:

0.000908

Gnomad4 NFE

AF:

0.000823

Gnomad4 OTH

AF:

0.00429

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over