X-11254716-CAAAAAAAAAAAA-CAAAA

Variant names:

• chrX-11254716-CAAAAAAAA-C
• NM_013427.3:c.589-17_589-10delTTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_013427.3(ARHGAP6):​c.589-17_589-10delTTTTTTTT variant causes a intron change. The variant allele was found at a frequency of 0.0000372 in 833,491 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 19)
  • Exomes 𝑓: 0.000037 (0 hom. 0 hem.)
• Consequence: ARHGAP6 NM_013427.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.92

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP6	NM_013427.3	c.589-17_589-10delTTTTTTTT		intron_variant	Intron 1 of 12	ENST00000337414.9	NP_038286.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP6	ENST00000337414.9	c.589-17_589-10delTTTTTTTT		intron_variant	Intron 1 of 12	1	NM_013427.3	ENSP00000338967.4

Frequencies

GnomAD3 genomes Cov.: 19

GnomAD4 exome AF: 0.0000372 AC: 31 AN: 833491 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 242065

Gnomad4 AFR exome AF: 0.0000528

Gnomad4 AMR exome AF: 0.000193

Gnomad4 ASJ exome AF: 0.0000898

Gnomad4 EAS exome AF: 0.000137

Gnomad4 SAS exome AF: 0.000309

Gnomad4 FIN exome AF: 0.0000909

Gnomad4 NFE exome AF: 0.0000216

Gnomad4 OTH exome AF: 0.0000291

GnomAD4 genome Cov.: 19

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-11272836;