X-11254716-C-CAAAAAAAAAA

Variant names:

• chrX-11254716-C-CAAAAAAAAAA
• rs751080433
• NM_013427.3:c.589-19_589-10dupTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_013427.3(ARHGAP6):​c.589-19_589-10dupTTTTTTTTTT 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 0.0 (0 hom., 0 hem., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: ARHGAP6 NM_013427.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013427.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP6	NM_013427.3	MANE Select	c.589-19_589-10dupTTTTTTTTTT		intron	N/A	NP_038286.2
	ARHGAP6	NM_001287242.2		c.49-19_49-10dupTTTTTTTTTT		intron	N/A	NP_001274171.1
	ARHGAP6	NM_013423.3		c.-21-19_-21-10dupTTTTTTTTTT		intron	N/A	NP_038267.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP6	ENST00000337414.9	TSL:1 MANE Select	c.589-10_589-9insTTTTTTTTTT		intron	N/A	ENSP00000338967.4
	ARHGAP6	ENST00000303025.10	TSL:1	c.-21-10_-21-9insTTTTTTTTTT		intron	N/A	ENSP00000302312.6
	ARHGAP6	ENST00000380736.5	TSL:1	c.-21-10_-21-9insTTTTTTTTTT		intron	N/A	ENSP00000370112.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 35325 Hom.: 0 Cov.: 19

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 35325 Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0 AN XY: 5877

African (AFR) AF: 0.00 AC: 0 AN: 9248

American (AMR) AF: 0.00 AC: 0 AN: 3292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 954

East Asian (EAS) AF: 0.00 AC: 0 AN: 1108

South Asian (SAS) AF: 0.00 AC: 0 AN: 641

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1101

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 68

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 18262

Other (OTH) AF: 0.00 AC: 0 AN: 457

Alfa AF: 0.000299 Hom.: 45

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.085

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs751080433; hg19: chrX-11272836;