4-147935609-G-C

Variant names:

• chr4-147935609-G-C
• rs6820696
• NM_024605.4:c.1229-4216G>C

Variant summary

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

The NM_024605.4(ARHGAP10):​c.1229-4216G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.912 in 152,204 control chromosomes in the GnomAD database, including 63,732 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 0.91 (63732 hom., cov: 31)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024605.4. 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.1229-4216G>C		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.1229-4216G>C		intron	N/A	ENSP00000336923.3
	ARHGAP10	ENST00000506054.5	TSL:1	n.6361-4216G>C		intron	N/A
	ARHGAP10	ENST00000507661.1	TSL:2	c.260-4216G>C		intron	N/A	ENSP00000422358.1

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138760 AN: 152086 Hom.: 63720 Cov.: 31

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.912 AC: 138819 AN: 152204 Hom.: 63732 Cov.: 31 AF XY: 0.914 AC XY: 67977 AN XY: 74410

African (AFR) AF: 0.792 AC: 32872 AN: 41498

American (AMR) AF: 0.960 AC: 14681 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3269 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5034 AN: 5170

South Asian (SAS) AF: 0.960 AC: 4637 AN: 4828

European-Finnish (FIN) AF: 0.934 AC: 9915 AN: 10610

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.960 AC: 65288 AN: 68018

Other (OTH) AF: 0.925 AC: 1949 AN: 2108

Alfa AF: 0.932 Hom.: 7743

Bravo AF: 0.909

Asia WGS AF: 0.953 AC: 3315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.12
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: rs6820696; hg19: chr4-148856760;