rs753387666
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_020433.5(JPH2):c.819C>T(p.Ala273Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A273A) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
JPH2
NM_020433.5 synonymous
NM_020433.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.49
Publications
0 publications found
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 17Inheritance: AD Classification: STRONG, MODERATE Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
- cardiomyopathy, dilated, 2EInheritance: Unknown, AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- hypertrophic cardiomyopathyInheritance: AD Classification: MODERATE Submitted by: ClinGen
- dilated cardiomyopathyInheritance: SD Classification: MODERATE Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP7
Synonymous conserved (PhyloP=-1.49 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00 AC: 0AN: 213848 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
213848
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1441782Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 715960
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1441782
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
715960
African (AFR)
AF:
AC:
0
AN:
33132
American (AMR)
AF:
AC:
0
AN:
42950
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25654
East Asian (EAS)
AF:
AC:
0
AN:
38890
South Asian (SAS)
AF:
AC:
0
AN:
83262
European-Finnish (FIN)
AF:
AC:
0
AN:
46242
Middle Eastern (MID)
AF:
AC:
0
AN:
5746
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1106070
Other (OTH)
AF:
AC:
0
AN:
59836
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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