rs17614025

Variant names:

• chr4-147889109-A-G
• rs17614025
• NM_024605.4:c.1034+7177A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000336498.8(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 ENST00000336498.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000336498.8. 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
	ARHGAP10	NM_024605.4	MANE Select	c.1034+7177A>G		intron	N/A	NP_078881.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP10	ENST00000336498.8	TSL:1 MANE Select	c.1034+7177A>G		intron	N/A	ENSP00000336923.3
	ARHGAP10	ENST00000506054.5	TSL:1	n.6166+7177A>G		intron	N/A
	ARHGAP10	ENST00000507661.1	TSL:2	c.65+7177A>G		intron	N/A	ENSP00000422358.1

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

African (AFR) AF: 0.224 AC: 9277 AN: 41476

American (AMR) AF: 0.763 AC: 11654 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2941 AN: 3472

East Asian (EAS) AF: 0.683 AC: 3531 AN: 5170

South Asian (SAS) AF: 0.835 AC: 4031 AN: 4830

European-Finnish (FIN) AF: 0.870 AC: 9225 AN: 10606

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62202 AN: 68020

Other (OTH) AF: 0.741 AC: 1564 AN: 2112

Alfa AF: 0.628 Hom.: 18455

Bravo AF: 0.660

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17614025; hg19: chr4-148810260;