rs201627219
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_002230.4(JUP):c.1159-13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000212 in 1,606,170 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002230.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JUP | NM_002230.4 | c.1159-13C>T | intron_variant | Intron 7 of 13 | ENST00000393931.8 | NP_002221.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JUP | ENST00000393931.8 | c.1159-13C>T | intron_variant | Intron 7 of 13 | 1 | NM_002230.4 | ENSP00000377508.3 | |||
JUP | ENST00000310706.9 | c.1159-13C>T | intron_variant | Intron 7 of 14 | 1 | ENSP00000311113.5 | ||||
JUP | ENST00000393930.5 | c.1159-13C>T | intron_variant | Intron 7 of 14 | 5 | ENSP00000377507.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249090Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134852
GnomAD4 exome AF: 0.0000186 AC: 27AN: 1453854Hom.: 0 Cov.: 29 AF XY: 0.0000166 AC XY: 12AN XY: 723822
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:1
1159-13C>T in intron 8 of JUP: This variant is not expected to have clinical sig nificance because a C>T change at this position does not diverge from the splice consensus sequence and is therefore unlikely to impact splicing. 1159-13C>T i n intron 8 of JUP (allele frequency = n/a) -
not provided Benign:1
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Naxos disease;C1969081:Arrhythmogenic right ventricular dysplasia 12 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at