17-41755074-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002230.4(JUP):c.*670G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 387,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000085 ( 0 hom. )
Consequence
JUP
NM_002230.4 3_prime_UTR
NM_002230.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.38
Genes affected
JUP (HGNC:6207): (junction plakoglobin) This gene encodes a major cytoplasmic protein which is the only known constituent common to submembranous plaques of both desmosomes and intermediate junctions. This protein forms distinct complexes with cadherins and desmosomal cadherins and is a member of the catenin family since it contains a distinct repeating amino acid motif called the armadillo repeat. Mutation in this gene has been associated with Naxos disease. Alternative splicing occurs in this gene; however, not all transcripts have been fully described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JUP | NM_002230.4 | c.*670G>A | 3_prime_UTR_variant | Exon 14 of 14 | ENST00000393931.8 | NP_002221.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JUP | ENST00000393931 | c.*670G>A | 3_prime_UTR_variant | Exon 14 of 14 | 1 | NM_002230.4 | ENSP00000377508.3 | |||
JUP | ENST00000310706 | c.*373G>A | 3_prime_UTR_variant | Exon 15 of 15 | 1 | ENSP00000311113.5 | ||||
JUP | ENST00000393930 | c.*373G>A | 3_prime_UTR_variant | Exon 15 of 15 | 5 | ENSP00000377507.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152030Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000848 AC: 2AN: 235872Hom.: 0 Cov.: 0 AF XY: 0.0000167 AC XY: 2AN XY: 119644
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 152030Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74262
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at