rs2635266

Variant names:

• chr4-147945375-G-A
• rs2635266
• NM_024605.4:c.1304-1242G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-147945375-G-A
• chr4-147945375-G-C
• chr4-147945375-G-T

Variant summary

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

The NM_024605.4(ARHGAP10):​c.1304-1242G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,046 control chromosomes in the GnomAD database, including 46,994 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 0.75 (46994 hom., cov: 31)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP10	NM_024605.4	c.1304-1242G>A		intron_variant	Intron 14 of 22	ENST00000336498.8	NP_078881.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP10	ENST00000336498.8	c.1304-1242G>A		intron_variant	Intron 14 of 22	1	NM_024605.4	ENSP00000336923.3
ARHGAP10	ENST00000506054.5	n.6436-1242G>A		intron_variant	Intron 8 of 16	1
ARHGAP10	ENST00000507661.1	c.335-1242G>A		intron_variant	Intron 5 of 12	2		ENSP00000422358.1

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114289 AN: 151928 Hom.: 46999 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.752 AC: 114308 AN: 152046 Hom.: 46994 Cov.: 31 AF XY: 0.756 AC XY: 56162 AN XY: 74330

African (AFR) AF: 0.391 AC: 16177 AN: 41422

American (AMR) AF: 0.794 AC: 12128 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3064 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3474 AN: 5160

South Asian (SAS) AF: 0.846 AC: 4075 AN: 4818

European-Finnish (FIN) AF: 0.908 AC: 9607 AN: 10580

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 62987 AN: 68002

Other (OTH) AF: 0.791 AC: 1670 AN: 2110

Alfa AF: 0.857 Hom.: 87173

Bravo AF: 0.722

Asia WGS AF: 0.720 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.58
DANN	Benign	0.51
PhyloP100		-0.10
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: rs2635266; hg19: chr4-148866526;