chr20-44114565-AGTGTGTGTGTGTGTGT-A

Variant names:

• chr20-44114565-AGTGTGTGTGTGTGTGT-A
• rs3037626
• NM_020433.5:c.*14+201_*14+216delACACACACACACACAC

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_020433.5(JPH2):​c.*14+201_*14+216delACACACACACACACAC 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 0.0035 (2 hom., cov: 0)
• Consequence: JPH2 NM_020433.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.794
• 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 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

ACMG classification

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

• BS2: High Homozygotes in GnomAd4 at 2 SD,AD,Unknown,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JPH2	NM_020433.5	c.*14+201_*14+216delACACACACACACACAC		intron_variant	Intron 5 of 5	ENST00000372980.4	NP_065166.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JPH2	ENST00000372980.4	c.*14+201_*14+216delACACACACACACACAC		intron_variant	Intron 5 of 5	5	NM_020433.5	ENSP00000362071.3

Frequencies

GnomAD3 genomes AF: 0.00352 AC: 499 AN: 141904 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00785

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00106

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.000649

Gnomad SAS AF: 0.00147

Gnomad FIN AF: 0.00298

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000689

Gnomad OTH AF: 0.000513

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00353 AC: 501 AN: 142002 Hom.: 2 Cov.: 0 AF XY: 0.00364 AC XY: 249 AN XY: 68390

African (AFR) AF: 0.00788 AC: 302 AN: 38316

American (AMR) AF: 0.00106 AC: 15 AN: 14168

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 102 AN: 3348

East Asian (EAS) AF: 0.000651 AC: 3 AN: 4608

South Asian (SAS) AF: 0.00147 AC: 6 AN: 4076

European-Finnish (FIN) AF: 0.00298 AC: 27 AN: 9054

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 270

European-Non Finnish (NFE) AF: 0.000689 AC: 45 AN: 65310

Other (OTH) AF: 0.000508 AC: 1 AN: 1970

Alfa AF: 0.00 Hom.: 238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs3037626; hg19: chr20-42743205;