16-87604287-CCTGCTGCTGCTGCTGCTG-C

Position:

• chr16-87604287-CCTGCTGCTGCTGCTGCTG-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP3 BP6 BS1 BS2

The NM_001271604.4(JPH3):​c.455_472delCTGCTGCTGCTGCTGCTG​(p.Ala152_Ala157del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,432,806 control chromosomes in the GnomAD database, including 11 homozygotes. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.0059 (7 hom., cov: 0)
  • Exomes 𝑓: 0.00062 (4 hom.)
• Consequence: JPH3 NM_001271604.4 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966

Genes affected

JPH3 (HGNC:14203): (junctophilin 3) 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. CAG/CTG repeat expansion from normally 6-28 repeats to 40-59 repeats in the 3' UTR of this gene have been associated with Huntington disease-like 2 (HDL2). This gene is a member of the junctophilin gene family. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2016]

JPH3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001271604.4
• BP6: Variant 16-87604287-CCTGCTGCTGCTGCTGCTG-C is Benign according to our data. Variant chr16-87604287-CCTGCTGCTGCTGCTGCTG-C is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00594 (892/150066) while in subpopulation AFR AF= 0.0196 (797/40668). AF 95% confidence interval is 0.0185. There are 7 homozygotes in gnomad4. There are 426 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 892 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JPH3	NM_020655.4	c.382+784_382+801delCTGCTGCTGCTGCTGCTG		intron_variant		ENST00000284262.3	NP_065706.2
JPH3	NM_001271604.4	c.455_472delCTGCTGCTGCTGCTGCTG	p.Ala152_Ala157del	disruptive_inframe_deletion	2/2		NP_001258533.1
JPH3	NM_001271605.3	c.*153_*170delCTGCTGCTGCTGCTGCTG		3_prime_UTR_variant	2/2		NP_001258534.1
JPH3	NR_073379.3	n.96+2382_96+2399delCTGCTGCTGCTGCTGCTG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JPH3	ENST00000284262.3	c.382+784_382+801delCTGCTGCTGCTGCTGCTG		intron_variant		1	NM_020655.4	ENSP00000284262.2
JPH3	ENST00000301008.5	n.715_732delCTGCTGCTGCTGCTGCTG		non_coding_transcript_exon_variant	2/2	1
JPH3	ENST00000537256.5	n.96+2382_96+2399delCTGCTGCTGCTGCTGCTG		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.00594 AC: 890 AN: 149958 Hom.: 7 Cov.: 0

Gnomad AFR AF: 0.0196

Gnomad AMI AF: 0.00111

Gnomad AMR AF: 0.00403

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000394

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000971

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000237

Gnomad OTH AF: 0.00633

GnomAD4 exome AF: 0.000619 AC: 794 AN: 1282740 Hom.: 4 AF XY: 0.000558 AC XY: 353 AN XY: 632954

Gnomad4 AFR exome AF: 0.0174

Gnomad4 AMR exome AF: 0.00142

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000166

Gnomad4 SAS exome AF: 0.000360

Gnomad4 FIN exome AF: 0.000170

Gnomad4 NFE exome AF: 0.000137

Gnomad4 OTH exome AF: 0.00131

GnomAD4 genome AF: 0.00594 AC: 892 AN: 150066 Hom.: 7 Cov.: 0 AF XY: 0.00582 AC XY: 426 AN XY: 73222

Gnomad4 AFR AF: 0.0196

Gnomad4 AMR AF: 0.00403

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000395

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000971

Gnomad4 NFE AF: 0.000237

Gnomad4 OTH AF: 0.00626

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71156237; hg19: chr16-87637893;