17-41755121-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_002230.4(JUP):c.*623G>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 0.0165 in 397,316 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002230.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JUP | NM_002230.4 | c.*623G>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.*623G>A | 3_prime_UTR_variant | Exon 14 of 14 | 1 | NM_002230.4 | ENSP00000377508.3 | |||
JUP | ENST00000310706 | c.*326G>A | 3_prime_UTR_variant | Exon 15 of 15 | 1 | ENSP00000311113.5 | ||||
JUP | ENST00000393930 | c.*326G>A | 3_prime_UTR_variant | Exon 15 of 15 | 5 | ENSP00000377507.1 |
Frequencies
GnomAD3 genomes AF: 0.0144 AC: 2188AN: 152128Hom.: 25 Cov.: 32
GnomAD4 exome AF: 0.0178 AC: 4368AN: 245070Hom.: 51 Cov.: 0 AF XY: 0.0180 AC XY: 2241AN XY: 124342
GnomAD4 genome AF: 0.0144 AC: 2187AN: 152246Hom.: 25 Cov.: 32 AF XY: 0.0136 AC XY: 1010AN XY: 74440
ClinVar
Submissions by phenotype
Naxos disease Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
not provided Benign:1
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Arrhythmogenic right ventricular dysplasia 12 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at