GeneBe

rs3037626

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_020433.5(JPH2):​c.*14+185_*14+216delACACACACACACACACACACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000049 ( 0 hom., cov: 0)

Consequence

JPH2
NM_020433.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.794

Publications

0 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 Submitted by: Labcorp Genetics (formerly Invitae)
  • dilated cardiomyopathy
    Inheritance: SD, AR, AD Classification: STRONG, MODERATE, LIMITED Submitted by: ClinGen
  • 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

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020433.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
JPH2
NM_020433.5
MANE Select
c.*14+185_*14+216delACACACACACACACACACACACACACACACAC
intron
N/ANP_065166.2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
JPH2
ENST00000372980.4
TSL:5 MANE Select
c.*14+185_*14+216delACACACACACACACACACACACACACACACAC
intron
N/AENSP00000362071.3Q9BR39-1
JPH2
ENST00000900330.1
c.*199_*230delACACACACACACACACACACACACACACACAC
3_prime_UTR
Exon 5 of 5ENSP00000570389.1
JPH2
ENST00000900331.1
c.*14+185_*14+216delACACACACACACACACACACACACACACACAC
intron
N/AENSP00000570390.1

Frequencies

GnomAD3 genomes
AF:
0.0000493
AC:
7
AN:
141906
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000524
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:
0.0000765
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000493
AC:
7
AN:
141906
Hom.:
0
Cov.:
0
AF XY:
0.0000586
AC XY:
4
AN XY:
68274
show subpopulations
African (AFR)
AF:
0.0000524
AC:
2
AN:
38198
American (AMR)
AF:
0.00
AC:
0
AN:
14156
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3348
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4620
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4086
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9056
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
0.0000765
AC:
5
AN:
65320
Other (OTH)
AF:
0.00
AC:
0
AN:
1948
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.468
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs3037626; hg19: chr20-42743205; API