rs7896935

chr10-48575452-C-T

Variant summary

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

The NM_021226.4(ARHGAP22):c.234+7501G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0791 in 152,200 control chromosomes in the GnomAD database, including 593 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 0.079 (593 hom., cov: 33)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: ARHGAP22 NM_021226.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

ARHGAP22 (HGNC:30320): (Rho GTPase activating protein 22) This gene encodes a member of the GTPase activating protein family which activates a GTPase belonging to the RAS superfamily of small GTP-binding proteins. The encoded protein is insulin-responsive, is dependent on the kinase Akt and requires the Akt-dependent 14-3-3 binding protein which binds sequentially to two serine residues. The result of these interactions is regulation of cell motility. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGAP22	NM_021226.4	c.234+7501G>A		intron_variant		ENST00000249601.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGAP22	ENST00000249601.9	c.234+7501G>A		intron_variant		1	NM_021226.4	P4

Frequencies

GnomAD3 genomes AF: 0.0791 AC: 12035 AN: 152076 Hom.: 591 Cov.: 33

Gnomad AFR AF: 0.0196

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0681

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.0791 AC: 12035 AN: 152194 Hom.: 593 Cov.: 33 AF XY: 0.0811 AC XY: 6031 AN XY: 74408

Gnomad4 AFR AF: 0.0195

Gnomad4 AMR AF: 0.0988

Gnomad4 ASJ AF: 0.0415

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0669

Alfa AF: 0.0858 Hom.: 71

Bravo AF: 0.0705

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.8
Dann	Benign	0.77

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: rs7896935; hg19: chr10-49783497;