Genetic Variant NM_013427.3:c.589-17_589-10dupTTTTTTTT (chrX-11254716-C-CAAAAAAAA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_013427.3(ARHGAP6):c.589-17_589-10dupTTTTTTTT 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)

Exomes 𝑓: 0.0000012 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

ARHGAP6
NM_013427.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0850

Publications

0 publications found

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:

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ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ARHGAP6	NM_013427.3	MANE Select	c.589-17_589-10dupTTTTTTTT	intron	N/A	NP_038286.2
ARHGAP6	NM_001287242.2		c.49-17_49-10dupTTTTTTTT	intron	N/A	NP_001274171.1
ARHGAP6	NM_013423.3		c.-21-17_-21-10dupTTTTTTTT	intron	N/A	NP_038267.1

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

35323

Hom.:

Cov.:

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

AF:

0.00000120

AC:

AN:

833796

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

242246

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

18946

American (AMR)

AF:

0.0000964

AC:

AN:

10370

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11140

East Asian (EAS)

AF:

0.00

AC:

AN:

21880

South Asian (SAS)

AF:

0.00

AC:

AN:

19492

European-Finnish (FIN)

AF:

0.00

AC:

AN:

22017

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2016

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

693565

Other (OTH)

AF:

0.00

AC:

AN:

34370

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.275

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

35323

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

5877

African (AFR)

AF:

0.00

AC:

AN:

9246

American (AMR)

AF:

0.00

AC:

AN:

3292

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

954

East Asian (EAS)

AF:

0.00

AC:

AN:

1108

South Asian (SAS)

AF:

0.00

AC:

AN:

641

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1101

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

18262

Other (OTH)

AF:

0.00

AC:

AN:

457

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over