X-11254716-CAAAAAAAAAAAA-CAAAAAAAAAAAAA

Position:

• chrX-11254716-CAAAAAAAAAAAA-CAAAAAAAAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_013427.3(ARHGAP6):​c.589-10dupT 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 0.080 (92 hom., 185 hem., cov: 19)
  • Exomes 𝑓: 0.021 (2 hom. 14 hem.)
• Consequence: ARHGAP6 NM_013427.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP6	NM_013427.3	c.589-10dupT		intron_variant		ENST00000337414.9	NP_038286.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP6	ENST00000337414.9	c.589-10dupT		intron_variant		1	NM_013427.3	ENSP00000338967.4

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 2784 AN: 34775 Hom.: 93 Cov.: 19 AF XY: 0.0320 AC XY: 185 AN XY: 5785

Gnomad AFR AF: 0.0577

Gnomad AMI AF: 0.0215

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0596

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.105

GnomAD3 exomes AF: 0.0379 AC: 569 AN: 15013 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 991

Gnomad AFR exome AF: 0.0518

Gnomad AMR exome AF: 0.0695

Gnomad ASJ exome AF: 0.0573

Gnomad EAS exome AF: 0.0515

Gnomad SAS exome AF: 0.0504

Gnomad FIN exome AF: 0.00361

Gnomad NFE exome AF: 0.0314

Gnomad OTH exome AF: 0.0442

GnomAD4 exome AF: 0.0215 AC: 17218 AN: 801808 Hom.: 2 Cov.: 0 AF XY: 0.0000642 AC XY: 14 AN XY: 218190

Gnomad4 AFR exome AF: 0.0228

Gnomad4 AMR exome AF: 0.0567

Gnomad4 ASJ exome AF: 0.0196

Gnomad4 EAS exome AF: 0.0203

Gnomad4 SAS exome AF: 0.0216

Gnomad4 FIN exome AF: 0.0116

Gnomad4 NFE exome AF: 0.0213

Gnomad4 OTH exome AF: 0.0215

GnomAD4 genome AF: 0.0799 AC: 2778 AN: 34773 Hom.: 92 Cov.: 19 AF XY: 0.0320 AC XY: 185 AN XY: 5787

Gnomad4 AFR AF: 0.0576

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.0362

Gnomad4 NFE AF: 0.0660

Gnomad4 OTH AF: 0.103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs751080433; hg19: chrX-11272836;