11-100722807-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.781
Variant links:
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]

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ACMG classification

Classification made for transcript

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
ARHGAP42NM_152432.4 linkc.154+34975G>C intron_variant Intron 1 of 23 ENST00000298815.13 NP_689645.2 A6NI28
ARHGAP42NM_001367945.1 linkc.-429+34975G>C intron_variant Intron 1 of 25 NP_001354874.1
ARHGAP42XM_011542616.3 linkc.-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
ARHGAP42ENST00000298815.13 linkc.154+34975G>C intron_variant Intron 1 of 23 5 NM_152432.4 ENSP00000298815.7 A6NI28
ARHGAP42ENST00000524892.7 linkc.154+34975G>C intron_variant Intron 1 of 22 5 ENSP00000431776.1 E9PJK4

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs633185; hg19: chr11-100593538; API