Genetic Variant NM_002230.4:c.909+17T>C (chr17-41767362-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002230.4(JUP):c.909+17T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 1,611,860 control chromosomes in the GnomAD database, including 522,337 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.81 ( 50207 hom., cov: 32)

Exomes 𝑓: 0.80 ( 472130 hom. )

Consequence

JUP
NM_002230.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: -0.00800

Variant links:

Genes affected

JUP (HGNC:6207): (junction plakoglobin) This gene encodes a major cytoplasmic protein which is the only known constituent common to submembranous plaques of both desmosomes and intermediate junctions. This protein forms distinct complexes with cadherins and desmosomal cadherins and is a member of the catenin family since it contains a distinct repeating amino acid motif called the armadillo repeat. Mutation in this gene has been associated with Naxos disease. Alternative splicing occurs in this gene; however, not all transcripts have been fully described. [provided by RefSeq, Jul 2008]

JUP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 17-41767362-A-G is Benign according to our data. Variant chr17-41767362-A-G is described in ClinVar as [Benign]. Clinvar id is 258593.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-41767362-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JUP	NM_002230.4 link	c.909+17T>C		intron_variant	Intron 5 of 13	ENST00000393931.8	NP_002221.1	P14923A0A0S2Z487

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JUP	ENST00000393931.8 link	c.909+17T>C		intron_variant	Intron 5 of 13	1	NM_002230.4	ENSP00000377508.3		P14923

Frequencies

GnomAD3 genomes

AF:

0.808

AC:

122885

AN:

152080

Hom.:

50160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.886

Gnomad AMI

AF:

0.803

Gnomad AMR

AF:

0.678

Gnomad ASJ

AF:

0.789

Gnomad EAS

AF:

0.510

Gnomad SAS

AF:

0.790

Gnomad FIN

AF:

0.785

Gnomad MID

AF:

0.820

Gnomad NFE

AF:

0.818

Gnomad OTH

AF:

0.798

GnomAD3 exomes

AF:

0.751

AC:

188199

AN:

250442

Hom.:

72781

AF XY:

0.763

AC XY:

103377

AN XY:

135472

show subpopulations

Gnomad AFR exome

AF:

0.892

Gnomad AMR exome

AF:

0.531

Gnomad ASJ exome

AF:

0.803

Gnomad EAS exome

AF:

0.501

Gnomad SAS exome

AF:

0.799

Gnomad FIN exome

AF:

0.787

Gnomad NFE exome

AF:

0.814

Gnomad OTH exome

AF:

0.768

GnomAD4 exome

AF:

0.801

AC:

1169037

AN:

1459662

Hom.:

472130

Cov.:

AF XY:

0.802

AC XY:

582409

AN XY:

726206

show subpopulations

Gnomad4 AFR exome

AF:

0.890

Gnomad4 AMR exome

AF:

0.548

Gnomad4 ASJ exome

AF:

0.797

Gnomad4 EAS exome

AF:

0.509

Gnomad4 SAS exome

AF:

0.800

Gnomad4 FIN exome

AF:

0.788

Gnomad4 NFE exome

AF:

0.820

Gnomad4 OTH exome

AF:

0.793

GnomAD4 genome

AF:

0.808

AC:

122992

AN:

152198

Hom.:

50207

Cov.:

AF XY:

0.801

AC XY:

59600

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.886

Gnomad4 AMR

AF:

0.677

Gnomad4 ASJ

AF:

0.789

Gnomad4 EAS

AF:

0.510

Gnomad4 SAS

AF:

0.792

Gnomad4 FIN

AF:

0.785

Gnomad4 NFE

AF:

0.818

Gnomad4 OTH

AF:

0.798

Alfa

AF:

0.815

Hom.:

9313

Bravo

AF:

0.798

Asia WGS

AF:

0.683

AC:

2379

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:7

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 12, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Naxos disease

Benign:1

Aug 19, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiomyopathy

Benign:1

Sep 23, 2022

Cohesion Phenomics

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Arrhythmogenic right ventricular dysplasia 12

Benign:1

Aug 19, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Naxos disease;C1969081:Arrhythmogenic right ventricular dysplasia 12

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

3.0

DANN

Benign

0.74

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