Variant rs1889532 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000495070.2(ARHGEF2):c.198+1396T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,020 control chromosomes in the GnomAD database, including 7,050 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 0.28 ( 7042 hom., cov: 31)

Exomes 𝑓: 0.34 ( 8 hom. )

Consequence

ARHGEF2
ENST00000495070.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.191

Variant links:

Genes affected

ARHGEF2 (HGNC:682): (Rho/Rac guanine nucleotide exchange factor 2) Rho GTPases play a fundamental role in numerous cellular processes that are initiated by extracellular stimuli that work through G protein coupled receptors. The encoded protein may form complex with G proteins and stimulate rho-dependent signals. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Jun 2009]

ARHGEF2 links:

ARHGEF2-AS2 (HGNC:55175): (ARHGEF2 antisense RNA 2)

ARHGEF2-AS2 links:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
ARHGEF2-AS2	NR_183459.1 link	n.901A>G	non_coding_transcript_exon_variant	2/2
ARHGEF2-AS2	NR_183460.1 link	n.1037A>G	non_coding_transcript_exon_variant	3/3
ARHGEF2-AS2	NR_183461.1 link	n.1038A>G	non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
ARHGEF2	ENST00000673475.1 link	c.492+1396T>C	intron_variant		ENSP00000500802.1	A0A5F9ZI21
ARHGEF2	ENST00000462460.6 link	c.198+1396T>C	intron_variant	5	ENSP00000476916.1	V9GYM8
ARHGEF2	ENST00000495070.2 link	c.198+1396T>C	intron_variant	4	ENSP00000476532.1	V9GY94

Frequencies

GnomAD3 genomes

AF:

0.284

AC:

43135

AN:

151814

Hom.:

7036

Cov.:

show subpopulations

Gnomad AFR

AF:

0.258

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.823

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.207

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.289

GnomAD4 exome

AF:

0.341

AC:

AN:

Hom.:

Cov.:

AF XY:

0.359

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.324

Gnomad4 OTH exome

AF:

0.200

GnomAD4 genome

AF:

0.284

AC:

43152

AN:

151932

Hom.:

7042

Cov.:

AF XY:

0.289

AC XY:

21483

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.258

Gnomad4 AMR

AF:

0.324

Gnomad4 ASJ

AF:

0.228

Gnomad4 EAS

AF:

0.824

Gnomad4 SAS

AF:

0.336

Gnomad4 FIN

AF:

0.256

Gnomad4 NFE

AF:

0.255

Gnomad4 OTH

AF:

0.285

Alfa

AF:

0.258

Hom.:

7715

Bravo

AF:

0.293

Asia WGS

AF:

0.537

AC:

1868

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.7

DANN

Benign

0.67

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over