rs193922903
Positions:
- chr16-87604287-CCTGCTGCTG-C
- chr16-87604287-CCTG-C
- chr16-87604287-C-CCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-CCTGCTGCTGCTGCTGCTGCTG-C
- chr16-87604287-C-CCTGCTGCTGCTGCTG
- chr16-87604287-CCTGCTGCTGCTGCTG-C
- chr16-87604287-CCTGCTGCTGCTG-C
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTG
- chr16-87604287-CCTGCTGCTGCTGCTGCTGCTGCTGCTG-C
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-CCTGCTGCTGCTGCTGCTGCTGCTG-C
- chr16-87604287-CCTGCTGCTGCTGCTGCTG-C
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTG
- chr16-87604287-C-CCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
- chr16-87604287-CCTGCTG-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP3BP6BS1BS2
The NM_001271604.4(JPH3):c.464_472delCTGCTGCTG(p.Ala155_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 0.0253 in 1,432,756 control chromosomes in the GnomAD database, including 377 homozygotes. Variant has been reported in Lovd as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.022 ( 51 hom., cov: 0)
Exomes 𝑓: 0.026 ( 326 hom. )
Consequence
JPH3
NM_001271604.4 disruptive_inframe_deletion
NM_001271604.4 disruptive_inframe_deletion
Scores
Not classified
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001271604.4
BP6
Variant 16-87604287-CCTGCTGCTG-C is Benign according to our data. Variant chr16-87604287-CCTGCTGCTG-C is described in Lovd as [Likely_benign]. Variant chr16-87604287-CCTGCTGCTG-C is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0219 (3281/150046) while in subpopulation NFE AF= 0.0295 (1992/67442). AF 95% confidence interval is 0.0285. There are 51 homozygotes in gnomad4. There are 1599 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 3281 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| JPH3 | NM_020655.4 | c.382+793_382+801delCTGCTGCTG | intron_variant | ENST00000284262.3 | NP_065706.2 | |||
| JPH3 | NM_001271604.4 | c.464_472delCTGCTGCTG | p.Ala155_Ala157del | disruptive_inframe_deletion | 2/2 | NP_001258533.1 | ||
| JPH3 | NM_001271605.3 | c.*162_*170delCTGCTGCTG | 3_prime_UTR_variant | 2/2 | NP_001258534.1 | |||
| JPH3 | NR_073379.3 | n.96+2391_96+2399delCTGCTGCTG | intron_variant |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| JPH3 | ENST00000284262.3 | c.382+793_382+801delCTGCTGCTG | intron_variant | 1 | NM_020655.4 | ENSP00000284262.2 | ||||
| JPH3 | ENST00000301008.5 | n.724_732delCTGCTGCTG | non_coding_transcript_exon_variant | 2/2 | 1 | |||||
| JPH3 | ENST00000537256.5 | n.96+2391_96+2399delCTGCTGCTG | intron_variant | 2 |
Frequencies
GnomAD3 genomes 0.0219 AC: 3279AN: 149940Hom.: 51 Cov.: 0
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GnomAD4 exome AF: 0.0257 AC: 33023AN: 1282710Hom.: 326 AF XY: 0.0248 AC XY: 15673AN XY: 632926
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GnomAD4 genome 0.0219 AC: 3281AN: 150046Hom.: 51 Cov.: 0 AF XY: 0.0218 AC XY: 1599AN XY: 73212
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ClinVar
Not reported inComputational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at