chr17-8289059-G-T

Position:

chr17-8289059-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The NM_016492.5(RANGRF):c.181G>T(p.Glu61*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00449 in 1,613,690 control chromosomes in the GnomAD database, including 29 homozygotes. Variant has been reported in ClinVar as Likely benign (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0036 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0046 ( 27 hom. )

Consequence

RANGRF
NM_016492.5 stop_gained

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 2.19

Variant links:

Genes affected

RANGRF (HGNC:17679): (RAN guanine nucleotide release factor) This gene encodes a protein that has been shown to function as a guanine nucleotide release factor in mouse and to regulate the expression and function of the Nav1.5 cardiac sodium channel in human. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]

RANGRF links:

SLC25A35 (HGNC:31921): (solute carrier family 25 member 35) SLC25A35 belongs to the SLC25 family of mitochondrial carrier proteins (Haitina et al., 2006 [PubMed 16949250]).[supplied by OMIM, Mar 2008]

SLC25A35 links:

RANGRF (HGNC:):

RANGRF links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP6

Variant 17-8289059-G-T is Benign according to our data. Variant chr17-8289059-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 190845.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-8289059-G-T is described in Lovd as [Benign]. Variant chr17-8289059-G-T is described in Lovd as [Likely_pathogenic].

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RANGRF	NM_016492.5 linkuse as main transcript	c.181G>T	p.Glu61*	stop_gained	2/5	ENST00000226105.11	NP_057576.2	Q9HD47-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RANGRF	ENST00000226105.11 linkuse as main transcript	c.181G>T	p.Glu61*	stop_gained	2/5	1	NM_016492.5	ENSP00000226105.6		Q9HD47-1

Frequencies

GnomAD3 genomes

AF:

0.00362

AC:

551

AN:

152238

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000844

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00248

Gnomad FIN

AF:

0.00988

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00534

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00400

AC:

996

AN:

248904

Hom.:

AF XY:

0.00390

AC XY:

527

AN XY:

134994

show subpopulations

Gnomad AFR exome

AF:

0.000750

Gnomad AMR exome

AF:

0.00101

Gnomad ASJ exome

AF:

0.000200

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00170

Gnomad FIN exome

AF:

0.0109

Gnomad NFE exome

AF:

0.00562

Gnomad OTH exome

AF:

0.00541

GnomAD4 exome

AF:

0.00458

AC:

6693

AN:

1461334

Hom.:

Cov.:

AF XY:

0.00452

AC XY:

3284

AN XY:

726980

show subpopulations

Gnomad4 AFR exome

AF:

0.000747

Gnomad4 AMR exome

AF:

0.00112

Gnomad4 ASJ exome

AF:

0.000230

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00189

Gnomad4 FIN exome

AF:

0.0104

Gnomad4 NFE exome

AF:

0.00508

Gnomad4 OTH exome

AF:

0.00399

GnomAD4 genome

AF:

0.00362

AC:

551

AN:

152356

Hom.:

Cov.:

AF XY:

0.00353

AC XY:

263

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.000842

Gnomad4 AMR

AF:

0.00105

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00248

Gnomad4 FIN

AF:

0.00988

Gnomad4 NFE

AF:

0.00534

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00457

Hom.:

Bravo

AF:

0.00298

TwinsUK

AF:

0.00458

AC:

ALSPAC

AF:

0.00389

AC:

ESP6500AA

AF:

0.00204

AC:

ESP6500EA

AF:

0.00535

AC:

ExAC

AF:

0.00395

AC:

479

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00551

EpiControl

AF:

0.00486

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2017	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Sep 16, 2024	Variant summary: RANGRF c.181G>T (p.Glu61X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, however current evidence is not sufficient to establish loss of function as a mechanism for disease. The variant allele was found at a frequency of 0.0045 in 1606716 control chromosomes in the gnomAD database (v4.1 dataset). , including 29 homozygotes. The observed variant frequency is approximately 700-fold of the estimated maximal expected allele frequency for a pathogenic variant in RANGRF causing Arrhythmia phenotype (6.3e-06). Although the variant was proposed to be related to various phenotypes in the literature, a recent study performing exhaustive genetic interpretation of reported variants in minor genes (potentially) associated with Brugada syndrome, classified the variant as benign (Campuzano_2019). The following publication have been ascertained in the context of this evaluation (PMID: 30821013). ClinVar contains an entry for this variant (Variation ID: 190845). Based on the evidence outlined above, the variant was classified as benign. -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

RANGRF-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 20, 2020

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

- -

Cardiac arrhythmia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.047

BayesDel_noAF

Pathogenic

0.30

CADD

Pathogenic

DANN

Uncertain

0.99

Eigen

Uncertain

0.40

Eigen_PC

Benign

0.15

FATHMM_MKL

Uncertain

0.83

Vest4

0.27

GERP RS

4.4

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.22

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.22

Position offset: -10

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