NM_020433.5:c.*14+205_*14+216delACACACACACAC

Variant names:

• chr20-44114565-AGTGTGTGTGTGT-A
• rs3037626
• NM_020433.5:c.*14+205_*14+216delACACACACACAC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_020433.5(JPH2):​c.*14+205_*14+216delACACACACACAC 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 0.016 (56 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: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0158 (2242/141978) while in subpopulation AFR AF = 0.0481 (1841/38300). AF 95% confidence interval is 0.0462. There are 56 homozygotes in GnomAd4. There are 1060 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 56 SD,AD,Unknown,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JPH2	NM_020433.5	c.*14+205_*14+216delACACACACACAC		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+205_*14+216delACACACACACAC		intron_variant	Intron 5 of 5	5	NM_020433.5	ENSP00000362071.3

Frequencies

GnomAD3 genomes AF: 0.0157 AC: 2234 AN: 141880 Hom.: 56 Cov.: 0

Gnomad AFR AF: 0.0480

Gnomad AMI AF: 0.0454

Gnomad AMR AF: 0.00551

Gnomad ASJ AF: 0.00568

Gnomad EAS AF: 0.00433

Gnomad SAS AF: 0.0115

Gnomad FIN AF: 0.000552

Gnomad MID AF: 0.0103

Gnomad NFE AF: 0.00245

Gnomad OTH AF: 0.0154

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

GnomAD4 genome AF: 0.0158 AC: 2242 AN: 141978 Hom.: 56 Cov.: 0 AF XY: 0.0155 AC XY: 1060 AN XY: 68384

African (AFR) AF: 0.0481 AC: 1841 AN: 38300

American (AMR) AF: 0.00551 AC: 78 AN: 14168

Ashkenazi Jewish (ASJ) AF: 0.00568 AC: 19 AN: 3348

East Asian (EAS) AF: 0.00434 AC: 20 AN: 4608

South Asian (SAS) AF: 0.0115 AC: 47 AN: 4072

European-Finnish (FIN) AF: 0.000552 AC: 5 AN: 9052

Middle Eastern (MID) AF: 0.00741 AC: 2 AN: 270

European-Non Finnish (NFE) AF: 0.00245 AC: 160 AN: 65308

Other (OTH) AF: 0.0152 AC: 30 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
Mutation Taster		=100/0	polymorphism

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;