rs16992796

Variant names:

• chr22-44787134-A-G
• rs16992796
• NM_181335.3:c.79+528A>G

Variant summary

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

The NM_181335.3(ARHGAP8):​c.79+528A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,992 control chromosomes in the GnomAD database, including 1,429 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 0.12 (1429 hom., cov: 33)
• Consequence: ARHGAP8 NM_181335.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

ARHGAP8 (HGNC:677): (Rho GTPase activating protein 8) This gene encodes a member of the RHOGAP family. GAP (GTPase-activating) family proteins participate in signaling pathways that regulate cell processes involved in cytoskeletal changes. GAP proteins alternate between an active (GTP-bound) and inactive (GDP-bound) state based on the GTP:GDP ratio in the cell. This family member is a multidomain protein that functions to promote Erk activation and cell motility. Alternative splicing results in multiple transcript variants. Read-through transcripts from the upstream proline rich 5, renal (PRR5) gene into this gene also exist, which led to the original description of PRR5 and ARHGAP8 being a single gene. [provided by RefSeq, Nov 2010]

PRR5-ARHGAP8 (HGNC:34512): (PRR5-ARHGAP8 readthrough) The PRR5-ARHGAP8 mRNA is an infrequent but naturally occurring read-through transcript of the neighboring proline rich 5, renal (PRR5) and Rho GTPase activating protein 8 (ARHGAP8) genes. The resulting fusion protein contains sequence identity with each individual gene product, and it includes domains characteristic of a RhoGAP protein. The significance of this read-through transcript and the function of its protein product have not yet been determined. [provided by RefSeq, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP8	NM_181335.3	c.79+528A>G		intron_variant	Intron 2 of 11	ENST00000356099.11	NP_851852.2
PRR5-ARHGAP8	NM_181334.6	c.472+528A>G		intron_variant	Intron 5 of 14		NP_851851.3
ARHGAP8	NM_001017526.2	c.79+528A>G		intron_variant	Intron 2 of 12		NP_001017526.1
ARHGAP8	NM_001198726.2	c.79+528A>G		intron_variant	Intron 2 of 10		NP_001185655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP8	ENST00000356099.11	c.79+528A>G		intron_variant	Intron 2 of 11	1	NM_181335.3	ENSP00000348407.6
PRR5-ARHGAP8	ENST00000352766.11	c.841+528A>G		intron_variant	Intron 8 of 16	2		ENSP00000262731.11

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17532 AN: 151876 Hom.: 1428 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0871

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.115 AC: 17549 AN: 151992 Hom.: 1429 Cov.: 33 AF XY: 0.114 AC XY: 8457 AN XY: 74328

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.0858

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0870

Gnomad4 SAS AF: 0.0909

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.0611

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0725 Hom.: 808

Bravo AF: 0.120

Asia WGS AF: 0.110 AC: 385 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.30
DANN	Benign	0.52

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: rs16992796; hg19: chr22-45183014;