GeneBe

rs56170305

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_020433.5(JPH2):​c.*14+173A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 27)
Failed GnomAD Quality Control

Consequence

JPH2
NM_020433.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.507

Publications

3 publications found
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 Gene-Disease associations (from GenCC):
  • hypertrophic cardiomyopathy 17
    Inheritance: AD Classification: STRONG, MODERATE Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
  • cardiomyopathy, dilated, 2E
    Inheritance: Unknown, AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
  • hypertrophic cardiomyopathy
    Inheritance: AD Classification: MODERATE Submitted by: ClinGen
  • dilated cardiomyopathy
    Inheritance: SD Classification: MODERATE Submitted by: ClinGen

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
JPH2NM_020433.5 linkc.*14+173A>T intron_variant Intron 5 of 5 ENST00000372980.4 NP_065166.2 Q9BR39-1Q86VZ3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
JPH2ENST00000372980.4 linkc.*14+173A>T intron_variant Intron 5 of 5 5 NM_020433.5 ENSP00000362071.3 Q9BR39-1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
144072
Hom.:
0
Cov.:
27
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
144172
Hom.:
0
Cov.:
27
AF XY:
0.00
AC XY:
0
AN XY:
69992
African (AFR)
AF:
0.00
AC:
0
AN:
38840
American (AMR)
AF:
0.00
AC:
0
AN:
14346
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3362
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4578
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4372
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9756
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
274
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
65748
Other (OTH)
AF:
0.00
AC:
0
AN:
2014
Alfa
AF:
0.00
Hom.:
2487

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
1.0
DANN
Benign
0.74
PhyloP100
-0.51

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

Other links and lift over

dbSNP: rs56170305; hg19: chr20-42743249; API