Variant 9-35661946-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_032818.3(ARHGEF39):c.*41T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0938 in 1,603,722 control chromosomes in the GnomAD database, including 7,981 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.072 ( 471 hom., cov: 33)

Exomes 𝑓: 0.096 ( 7510 hom. )

Consequence

ARHGEF39
NM_032818.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0370

Variant links:

Genes affected

ARHGEF39 (HGNC:25909): (Rho guanine nucleotide exchange factor 39) Predicted to enable guanyl-nucleotide exchange factor activity. Involved in positive regulation of cell migration. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ARHGEF39 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 9-35661946-A-C is Benign according to our data. Variant chr9-35661946-A-C is described in ClinVar as [Benign]. Clinvar id is 1289970.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARHGEF39	NM_032818.3 linkuse as main transcript	c.*41T>G		3_prime_UTR_variant	9/9	ENST00000378387.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARHGEF39	ENST00000378387.4 linkuse as main transcript	c.*41T>G		3_prime_UTR_variant	9/9	1	NM_032818.3	P1	Q8N4T4-1

Frequencies

GnomAD3 genomes

AF:

0.0723

AC:

11000

AN:

152158

Hom.:

471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0272

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.0755

Gnomad ASJ

AF:

0.0496

Gnomad EAS

AF:

0.0291

Gnomad SAS

AF:

0.0512

Gnomad FIN

AF:

0.0630

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.0794

GnomAD3 exomes

AF:

0.0780

AC:

19162

AN:

245732

Hom.:

915

AF XY:

0.0779

AC XY:

10352

AN XY:

132844

show subpopulations

Gnomad AFR exome

AF:

0.0283

Gnomad AMR exome

AF:

0.0723

Gnomad ASJ exome

AF:

0.0539

Gnomad EAS exome

AF:

0.0329

Gnomad SAS exome

AF:

0.0560

Gnomad FIN exome

AF:

0.0612

Gnomad NFE exome

AF:

0.106

Gnomad OTH exome

AF:

0.0731

GnomAD4 exome

AF:

0.0961

AC:

139458

AN:

1451446

Hom.:

7510

Cov.:

AF XY:

0.0953

AC XY:

68855

AN XY:

722190

show subpopulations

Gnomad4 AFR exome

AF:

0.0250

Gnomad4 AMR exome

AF:

0.0707

Gnomad4 ASJ exome

AF:

0.0528

Gnomad4 EAS exome

AF:

0.0239

Gnomad4 SAS exome

AF:

0.0582

Gnomad4 FIN exome

AF:

0.0598

Gnomad4 NFE exome

AF:

0.108

Gnomad4 OTH exome

AF:

0.0873

GnomAD4 genome

AF:

0.0723

AC:

11007

AN:

152276

Hom.:

471

Cov.:

AF XY:

0.0694

AC XY:

5165

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.0271

Gnomad4 AMR

AF:

0.0756

Gnomad4 ASJ

AF:

0.0496

Gnomad4 EAS

AF:

0.0291

Gnomad4 SAS

AF:

0.0510

Gnomad4 FIN

AF:

0.0630

Gnomad4 NFE

AF:

0.106

Gnomad4 OTH

AF:

0.0814

Alfa

AF:

0.0961

Hom.:

1009

Bravo

AF:

0.0728

Asia WGS

AF:

0.0540

AC:

187

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 18, 2019

This variant is associated with the following publications: (PMID: 28289279) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over