rs7268512

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_020433.5(JPH2):c.1179C>T(p.His393His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0884 in 1,608,650 control chromosomes in the GnomAD database, including 6,948 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.082 ( 563 hom., cov: 33)

Exomes 𝑓: 0.089 ( 6385 hom. )

Consequence

JPH2
NM_020433.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.0590

Variant links:

Genes affected

JPH2 (HGNC:14202): (junctophilin 2) Junctional complexes between the plasma membrane and endoplasmic/sarcoplasmic reticulum are a common feature of all excitable cell types and mediate cross talk between cell surface and intracellular ion channels. The protein encoded by this gene is a component of junctional complexes and is composed of a C-terminal hydrophobic segment spanning the endoplasmic/sarcoplasmic reticulum membrane and a remaining cytoplasmic domain that shows specific affinity for the plasma membrane. This gene is a member of the junctophilin gene family. Alternative splicing has been observed at this locus and two variants encoding distinct isoforms are described. [provided by RefSeq, Jul 2008]

JPH2 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=-0.55).

BP6

Variant 20-44118614-G-A is Benign according to our data. Variant chr20-44118614-G-A is described in ClinVar as [Benign]. Clinvar id is 137606.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-44118614-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.059 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JPH2	NM_020433.5 link	c.1179C>T	p.His393His	synonymous_variant	Exon 3 of 6	ENST00000372980.4	NP_065166.2	Q9BR39-1Q86VZ3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JPH2	ENST00000372980.4 link	c.1179C>T	p.His393His	synonymous_variant	Exon 3 of 6	5	NM_020433.5	ENSP00000362071.3		Q9BR39-1

Frequencies

GnomAD3 genomes

AF:

0.0823

AC:

12519

AN:

152162

Hom.:

563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0795

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.0558

Gnomad ASJ

AF:

0.0597

Gnomad EAS

AF:

0.0110

Gnomad SAS

AF:

0.0257

Gnomad FIN

AF:

0.0745

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.0822

GnomAD3 exomes

AF:

0.0688

AC:

17051

AN:

247884

Hom.:

738

AF XY:

0.0685

AC XY:

9201

AN XY:

134326

show subpopulations

Gnomad AFR exome

AF:

0.0782

Gnomad AMR exome

AF:

0.0424

Gnomad ASJ exome

AF:

0.0551

Gnomad EAS exome

AF:

0.00861

Gnomad SAS exome

AF:

0.0289

Gnomad FIN exome

AF:

0.0792

Gnomad NFE exome

AF:

0.0949

Gnomad OTH exome

AF:

0.0790

GnomAD4 exome

AF:

0.0890

AC:

129683

AN:

1456370

Hom.:

6385

Cov.:

AF XY:

0.0875

AC XY:

63385

AN XY:

724738

show subpopulations

Gnomad4 AFR exome

AF:

0.0774

Gnomad4 AMR exome

AF:

0.0432

Gnomad4 ASJ exome

AF:

0.0564

Gnomad4 EAS exome

AF:

0.00499

Gnomad4 SAS exome

AF:

0.0299

Gnomad4 FIN exome

AF:

0.0766

Gnomad4 NFE exome

AF:

0.101

Gnomad4 OTH exome

AF:

0.0812

GnomAD4 genome

AF:

0.0822

AC:

12515

AN:

152280

Hom.:

563

Cov.:

AF XY:

0.0797

AC XY:

5938

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0793

Gnomad4 AMR

AF:

0.0556

Gnomad4 ASJ

AF:

0.0597

Gnomad4 EAS

AF:

0.0106

Gnomad4 SAS

AF:

0.0257

Gnomad4 FIN

AF:

0.0745

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.0814

Alfa

AF:

0.0891

Hom.:

191

Bravo

AF:

0.0811

Asia WGS

AF:

0.0240

AC:

AN:

3478

EpiCase

AF:

0.0951

EpiControl

AF:

0.0917

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Nov 18, 2013

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. -

Nov 24, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

His393His in exon 3 of JPH2: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. It has been identified in 10.3% (883/8600) of E uropean American chromosomes from a broad population by the NHLBI Exome Sequenci ng Project (http://evs.gs.washington.edu/EVS; dbSNP rs7268512). -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Hypertrophic cardiomyopathy 17

Benign:1

Sep 21, 2015

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

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hypertrophic cardiomyopathy

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype

Benign:1

Jun 19, 2015

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

5.2

DANN

Benign

0.69

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