Variant 12-48940016-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000256682.9(ARF3):c.240C>T(p.His80His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0711 in 1,613,860 control chromosomes in the GnomAD database, including 5,259 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.051 ( 295 hom., cov: 32)

Exomes 𝑓: 0.073 ( 4964 hom. )

Consequence

ARF3
ENST00000256682.9 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.413

Variant links:

Genes affected

ARF3 (HGNC:654): (ADP ribosylation factor 3) ADP-ribosylation factor 3 (ARF3) is a member of the human ARF gene family. These genes encode small guanine nucleotide-binding proteins that stimulate the ADP-ribosyltransferase activity of cholera toxin and play a role in vesicular trafficking and as activators of phospholipase D. The gene products include 6 ARF proteins and 11 ARF-like proteins and constitute one family of the RAS superfamily. The ARF proteins are categorized as class I (ARF1, ARF2,and ARF3), class II (ARF4 and ARF5) and class III (ARF6) and members of each class share a common gene organization. [provided by RefSeq, Oct 2022]

ARF3 links:

ENSG00000272822 (HGNC:):

ENSG00000272822 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 12-48940016-G-A is Benign according to our data. Variant chr12-48940016-G-A is described in ClinVar as [Benign]. Clinvar id is 1304691.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.413 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARF3	NM_001659.3 linkuse as main transcript	c.240C>T	p.His80His	synonymous_variant	3/5	ENST00000256682.9	NP_001650.1	P61204-1A0A024R0Y6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARF3	ENST00000256682.9 linkuse as main transcript	c.240C>T	p.His80His	synonymous_variant	3/5	1	NM_001659.3	ENSP00000256682.4		P61204-1
ENSG00000272822	ENST00000398092.4 linkuse as main transcript	c.240C>T	p.His80His	synonymous_variant	3/5	3		ENSP00000438507.1		F5H423

Frequencies

GnomAD3 genomes

AF:

0.0510

AC:

7766

AN:

152162

Hom.:

296

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0137

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0398

Gnomad ASJ

AF:

0.0757

Gnomad EAS

AF:

0.0100

Gnomad SAS

AF:

0.190

Gnomad FIN

AF:

0.0483

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0687

Gnomad OTH

AF:

0.0626

GnomAD3 exomes

AF:

0.0720

AC:

18115

AN:

251474

Hom.:

1066

AF XY:

0.0799

AC XY:

10857

AN XY:

135908

show subpopulations

Gnomad AFR exome

AF:

0.0122

Gnomad AMR exome

AF:

0.0404

Gnomad ASJ exome

AF:

0.0781

Gnomad EAS exome

AF:

0.00701

Gnomad SAS exome

AF:

0.195

Gnomad FIN exome

AF:

0.0503

Gnomad NFE exome

AF:

0.0707

Gnomad OTH exome

AF:

0.0827

GnomAD4 exome

AF:

0.0732

AC:

106930

AN:

1461580

Hom.:

4964

Cov.:

AF XY:

0.0771

AC XY:

56089

AN XY:

727116

show subpopulations

Gnomad4 AFR exome

AF:

0.0128

Gnomad4 AMR exome

AF:

0.0415

Gnomad4 ASJ exome

AF:

0.0788

Gnomad4 EAS exome

AF:

0.00463

Gnomad4 SAS exome

AF:

0.190

Gnomad4 FIN exome

AF:

0.0524

Gnomad4 NFE exome

AF:

0.0701

Gnomad4 OTH exome

AF:

0.0759

GnomAD4 genome

AF:

0.0510

AC:

7764

AN:

152280

Hom.:

295

Cov.:

AF XY:

0.0511

AC XY:

3805

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0136

Gnomad4 AMR

AF:

0.0396

Gnomad4 ASJ

AF:

0.0757

Gnomad4 EAS

AF:

0.00983

Gnomad4 SAS

AF:

0.190

Gnomad4 FIN

AF:

0.0483

Gnomad4 NFE

AF:

0.0686

Gnomad4 OTH

AF:

0.0624

Alfa

AF:

0.0628

Hom.:

228

Bravo

AF:

0.0454

Asia WGS

AF:

0.0920

AC:

317

AN:

3478

EpiCase

AF:

0.0704

EpiControl

AF:

0.0678

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

8.2

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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