11-100722807-G-C

Variant names:

• chr11-100722807-G-C
• rs633185
• NM_152432.4:c.154+34975G>C

Variant summary

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

The NM_152432.4(ARHGAP42):​c.154+34975G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,108 control chromosomes in the GnomAD database, including 39,173 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 0.71 (39173 hom., cov: 33)
• Consequence: ARHGAP42 NM_152432.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781

Genes affected

ARHGAP42 (HGNC:26545): (Rho GTPase activating protein 42) This gene encodes a Rho GTPase-activating protein (RhoGAP), and member of the GRAF or BAR-PH family of proteins. Expression of this gene is enriched in vascular smooth muscle cells and the encoded protein inhibits RhoA activity to regulate vascular tone and control blood pressure. A mutation in the first intron of this gene modulates its expression and is associated with reduced blood pressure in human patients with borderline hypertension. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP42	NM_152432.4	c.154+34975G>C		intron_variant	Intron 1 of 23	ENST00000298815.13	NP_689645.2
ARHGAP42	NM_001367945.1	c.-429+34975G>C		intron_variant	Intron 1 of 25		NP_001354874.1
ARHGAP42	XM_011542616.3	c.-9+7283G>C		intron_variant	Intron 1 of 23		XP_011540918.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP42	ENST00000298815.13	c.154+34975G>C		intron_variant	Intron 1 of 23	5	NM_152432.4	ENSP00000298815.7
ARHGAP42	ENST00000524892.7	c.154+34975G>C		intron_variant	Intron 1 of 22	5		ENSP00000431776.1

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108431 AN: 151988 Hom.: 39148 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.713 AC: 108518 AN: 152108 Hom.: 39173 Cov.: 33 AF XY: 0.707 AC XY: 52582 AN XY: 74370

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.720

Alfa AF: 0.689 Hom.: 17691

Bravo AF: 0.709

Asia WGS AF: 0.545 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.58

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: rs633185; hg19: chr11-100593538;