NM_020433.5:c.379+36A>T
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.379+36A>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)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
JPH2
NM_020433.5 intron
NM_020433.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.491
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]
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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=-0.76).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| JPH2 | NM_020433.5 | c.379+36A>T | intron_variant | Intron 1 of 5 | ENST00000372980.4 | NP_065166.2 | ||
| JPH2 | NM_175913.4 | c.379+36A>T | intron_variant | Intron 1 of 1 | NP_787109.2 | |||
| JPH2 | XM_006723833.5 | c.379+36A>T | intron_variant | Intron 1 of 1 | XP_006723896.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151484Hom.: 0 Cov.: 27
GnomAD3 genomes
AF:
AC:
0
AN:
151484
Hom.:
Cov.:
27
Gnomad AFR
AF:
Gnomad AMI
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Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
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Gnomad FIN
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Gnomad NFE
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Gnomad OTH
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1453920Hom.: 0 Cov.: 40 AF XY: 0.00 AC XY: 0AN XY: 723544
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1453920
Hom.:
Cov.:
40
AF XY:
AC XY:
0
AN XY:
723544
African (AFR)
AF:
AC:
0
AN:
33392
American (AMR)
AF:
AC:
0
AN:
44548
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26034
East Asian (EAS)
AF:
AC:
0
AN:
39696
South Asian (SAS)
AF:
AC:
0
AN:
86162
European-Finnish (FIN)
AF:
AC:
0
AN:
46858
Middle Eastern (MID)
AF:
AC:
0
AN:
5722
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111206
Other (OTH)
AF:
AC:
0
AN:
60302
GnomAD4 genome 0.00 AC: 0AN: 151484Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 73938
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
151484
Hom.:
Cov.:
27
AF XY:
AC XY:
0
AN XY:
73938
African (AFR)
AF:
AC:
0
AN:
41164
American (AMR)
AF:
AC:
0
AN:
15236
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5070
South Asian (SAS)
AF:
AC:
0
AN:
4792
European-Finnish (FIN)
AF:
AC:
0
AN:
10546
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67900
Other (OTH)
AF:
AC:
0
AN:
2084
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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