4-147766488-T-C

Variant names:

• chr4-147766488-T-C
• rs6822971
• NM_024605.4:c.154+34033T>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.154+34033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 151,356 control chromosomes in the GnomAD database, including 48,053 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 (48053 hom., cov: 27)
• Consequence: ARHGAP10 NM_024605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 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.154+34033T>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.154+34033T>C		intron	N/A	ENSP00000336923.3
	ARHGAP10	ENST00000510379.1	TSL:2	n.393+34033T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.747 AC: 112928 AN: 151238 Hom.: 48057 Cov.: 27

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.746 AC: 112931 AN: 151356 Hom.: 48053 Cov.: 27 AF XY: 0.752 AC XY: 55631 AN XY: 73944

African (AFR) AF: 0.299 AC: 12295 AN: 41188

American (AMR) AF: 0.857 AC: 13025 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3145 AN: 3468

East Asian (EAS) AF: 0.903 AC: 4575 AN: 5066

South Asian (SAS) AF: 0.807 AC: 3854 AN: 4778

European-Finnish (FIN) AF: 0.979 AC: 10244 AN: 10464

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63177 AN: 67892

Other (OTH) AF: 0.777 AC: 1627 AN: 2094

Alfa AF: 0.821 Hom.: 9027

Bravo AF: 0.717

Asia WGS AF: 0.807 AC: 2807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.66
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: rs6822971; hg19: chr4-148687639;