Variant rs2364403 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001162383.2(ARHGEF2):c.1546-79C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 1,432,420 control chromosomes in the GnomAD database, including 48,704 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 0.26 ( 6104 hom., cov: 33)

Exomes 𝑓: 0.23 ( 42600 hom. )

Consequence

ARHGEF2
NM_001162383.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.587

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:

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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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARHGEF2	NM_001162383.2 linkuse as main transcript	c.1546-79C>T		intron_variant		ENST00000361247.9	NP_001155855.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARHGEF2	ENST00000361247.9 linkuse as main transcript	c.1546-79C>T		intron_variant		1	NM_001162383.2	ENSP00000354837	P4	Q92974-1

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39509

AN:

152044

Hom.:

6092

Cov.:

show subpopulations

Gnomad AFR

AF:

0.289

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.775

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.194

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.263

GnomAD4 exome

AF:

0.234

AC:

299159

AN:

1280258

Hom.:

42600

AF XY:

0.234

AC XY:

147807

AN XY:

633004

show subpopulations

Gnomad4 AFR exome

AF:

0.292

Gnomad4 AMR exome

AF:

0.395

Gnomad4 ASJ exome

AF:

0.200

Gnomad4 EAS exome

AF:

0.787

Gnomad4 SAS exome

AF:

0.285

Gnomad4 FIN exome

AF:

0.193

Gnomad4 NFE exome

AF:

0.204

Gnomad4 OTH exome

AF:

0.254

GnomAD4 genome

AF:

0.260

AC:

39543

AN:

152162

Hom.:

6104

Cov.:

AF XY:

0.263

AC XY:

19594

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.288

Gnomad4 AMR

AF:

0.298

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.775

Gnomad4 SAS

AF:

0.301

Gnomad4 FIN

AF:

0.194

Gnomad4 NFE

AF:

0.207

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.213

Hom.:

3126

Bravo

AF:

0.276

Asia WGS

AF:

0.512

AC:

1779

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

4.1

DANN

Benign

0.23

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.

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