chrX-11254716-C-CAA

Position:

• chrX-11254716-C-CAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_013427.3(ARHGAP6):​c.589-11_589-10dupTT 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 0.025 (8 hom., 50 hem., cov: 19)
  • Exomes 𝑓: 0.0051 (2 hom. 11 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.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0253 (892/35239) while in subpopulation NFE AF= 0.0402 (732/18216). AF 95% confidence interval is 0.0378. There are 8 homozygotes in gnomad4. There are 50 alleles in male gnomad4 subpopulation. Median coverage is 19. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP6	NM_013427.3	c.589-11_589-10dupTT		intron_variant		ENST00000337414.9	NP_038286.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP6	ENST00000337414.9	c.589-11_589-10dupTT		intron_variant		1	NM_013427.3	ENSP00000338967.4

Frequencies

GnomAD3 genomes AF: 0.0254 AC: 894 AN: 35243 Hom.: 8 Cov.: 19 AF XY: 0.00852 AC XY: 50 AN XY: 5867

Gnomad AFR AF: 0.00607

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0116

Gnomad ASJ AF: 0.0116

Gnomad EAS AF: 0.00452

Gnomad SAS AF: 0.0392

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0294

Gnomad NFE AF: 0.0403

Gnomad OTH AF: 0.0197

GnomAD4 exome AF: 0.00511 AC: 4193 AN: 820541 Hom.: 2 Cov.: 0 AF XY: 0.0000466 AC XY: 11 AN XY: 235901

Gnomad4 AFR exome AF: 0.00240

Gnomad4 AMR exome AF: 0.00634

Gnomad4 ASJ exome AF: 0.00190

Gnomad4 EAS exome AF: 0.00124

Gnomad4 SAS exome AF: 0.00781

Gnomad4 FIN exome AF: 0.00210

Gnomad4 NFE exome AF: 0.00542

Gnomad4 OTH exome AF: 0.00414

GnomAD4 genome AF: 0.0253 AC: 892 AN: 35239 Hom.: 8 Cov.: 19 AF XY: 0.00852 AC XY: 50 AN XY: 5869

Gnomad4 AFR AF: 0.00606

Gnomad4 AMR AF: 0.0116

Gnomad4 ASJ AF: 0.0116

Gnomad4 EAS AF: 0.00455

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.0402

Gnomad4 OTH AF: 0.0194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;