17-41755458-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002230.4(JUP):c.*286C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 427,580 control chromosomes in the GnomAD database, including 297 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002230.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JUP | NM_002230.4 | c.*286C>T | 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.*286C>T | 3_prime_UTR_variant | Exon 14 of 14 | 1 | NM_002230.4 | ENSP00000377508.3 | |||
JUP | ENST00000310706.9 | c.*15-26C>T | intron_variant | Intron 14 of 14 | 1 | ENSP00000311113.5 | ||||
JUP | ENST00000393930.5 | c.*15-26C>T | intron_variant | Intron 14 of 14 | 5 | ENSP00000377507.1 |
Frequencies
GnomAD3 genomes AF: 0.0306 AC: 4645AN: 151968Hom.: 246 Cov.: 32
GnomAD4 exome AF: 0.00415 AC: 1143AN: 275494Hom.: 50 Cov.: 0 AF XY: 0.00356 AC XY: 500AN XY: 140274
GnomAD4 genome AF: 0.0306 AC: 4655AN: 152086Hom.: 247 Cov.: 32 AF XY: 0.0292 AC XY: 2168AN XY: 74362
ClinVar
Submissions by phenotype
not provided Benign:2
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Naxos disease Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Arrhythmogenic right ventricular dysplasia 12 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at