chr17-41757472-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_002230.4(JUP):c.1989C>T(p.Arg663=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,614,222 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 (★★). Synonymous variant affecting the same amino acid position (i.e. R663R) has been classified as Likely benign.
Frequency
Consequence
NM_002230.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JUP | NM_002230.4 | c.1989C>T | p.Arg663= | synonymous_variant | 12/14 | ENST00000393931.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JUP | ENST00000393931.8 | c.1989C>T | p.Arg663= | synonymous_variant | 12/14 | 1 | NM_002230.4 | P1 | |
JUP | ENST00000310706.9 | c.1989C>T | p.Arg663= | synonymous_variant | 12/15 | 1 | P1 | ||
JUP | ENST00000393930.5 | c.1989C>T | p.Arg663= | synonymous_variant | 12/15 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000596 AC: 15AN: 251492Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135922
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461890Hom.: 0 Cov.: 38 AF XY: 0.0000316 AC XY: 23AN XY: 727246
GnomAD4 genome AF: 0.000105 AC: 16AN: 152332Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 19, 2012 | p.Arg663Arg in exon 12 of JUP: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 1/3738 African Amer ican chromosomes from a broad population by the NHLBI Exome Sequencing Project ( http://evs.gs.washington.edu/EVS; dbSNP rs145175985). - |
JUP-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 10, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 08, 2019 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Naxos disease;C1969081:Arrhythmogenic right ventricular dysplasia 12 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at