20-44114565-AGTGT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_020433.5(JPH2):​c.*14+213_*14+216delACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.078 ( 576 hom., cov: 0)

Consequence

JPH2
NM_020433.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.794
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 20-44114565-AGTGT-A is Benign according to our data. Variant chr20-44114565-AGTGT-A is described in ClinVar as [Benign]. Clinvar id is 1291506.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
JPH2NM_020433.5 linkc.*14+213_*14+216delACAC 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+213_*14+216delACAC intron_variant Intron 5 of 5 5 NM_020433.5 ENSP00000362071.3 Q9BR39-1

Frequencies

GnomAD3 genomes
AF:
0.0775
AC:
10979
AN:
141654
Hom.:
575
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.152
Gnomad AMI
AF:
0.00680
Gnomad AMR
AF:
0.0526
Gnomad ASJ
AF:
0.0648
Gnomad EAS
AF:
0.186
Gnomad SAS
AF:
0.106
Gnomad FIN
AF:
0.0390
Gnomad MID
AF:
0.0856
Gnomad NFE
AF:
0.0375
Gnomad OTH
AF:
0.0716
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0775
AC:
10988
AN:
141750
Hom.:
576
Cov.:
0
AF XY:
0.0775
AC XY:
5291
AN XY:
68270
show subpopulations
Gnomad4 AFR
AF:
0.151
Gnomad4 AMR
AF:
0.0525
Gnomad4 ASJ
AF:
0.0648
Gnomad4 EAS
AF:
0.186
Gnomad4 SAS
AF:
0.105
Gnomad4 FIN
AF:
0.0390
Gnomad4 NFE
AF:
0.0375
Gnomad4 OTH
AF:
0.0729

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Aug 15, 2019
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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.

Other links and lift over

dbSNP: rs3037626; hg19: chr20-42743205; API