rs17614025

Positions:

• chr4-147889109-A-G
• chr4-147889109-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024605.4(ARHGAP10):​c.1034+7177A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,172 control chromosomes in the GnomAD database, including 43,296 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.69 (43296 hom., cov: 32)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

Genes affected

ARHGAP10 (HGNC:26099): (Rho GTPase activating protein 10) Predicted to enable GTPase activator activity. Predicted to be involved in cytoskeleton organization and negative regulation of apoptotic process. Predicted to be located in perinuclear region of cytoplasm and plasma membrane. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGAP10	NM_024605.4	c.1034+7177A>G		intron_variant		ENST00000336498.8	NP_078881.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGAP10	ENST00000336498.8	c.1034+7177A>G		intron_variant		1	NM_024605.4	ENSP00000336923	P1
ARHGAP10	ENST00000506054.5	n.6166+7177A>G		intron_variant, non_coding_transcript_variant		1
ARHGAP10	ENST00000507661.1	c.66+7177A>G		intron_variant		2		ENSP00000422358

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105558 AN: 152054 Hom.: 43308 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.739

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.694 AC: 105546 AN: 152172 Hom.: 43296 Cov.: 32 AF XY: 0.697 AC XY: 51857 AN XY: 74418

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.741

Alfa AF: 0.739 Hom.: 11527

Bravo AF: 0.660

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.75

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: rs17614025; hg19: chr4-148810260;