rs8215
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001135048.2(JDP2):c.*339T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 206,218 control chromosomes in the GnomAD database, including 23,365 homozygotes. 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 0.46 ( 16510 hom., cov: 33)
Exomes 𝑓: 0.49 ( 6855 hom. )
Consequence
JDP2
NM_001135048.2 3_prime_UTR
NM_001135048.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0400
Genes affected
JDP2 (HGNC:17546): (Jun dimerization protein 2) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JDP2 | NM_001135048.2 | c.*339T>C | 3_prime_UTR_variant | 4/4 | ENST00000651602.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JDP2 | ENST00000651602.1 | c.*339T>C | 3_prime_UTR_variant | 4/4 | NM_001135048.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.457 AC: 69472AN: 152006Hom.: 16509 Cov.: 33
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GnomAD4 exome AF: 0.493 AC: 26646AN: 54094Hom.: 6855 Cov.: 0 AF XY: 0.495 AC XY: 13718AN XY: 27732
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GnomAD4 genome ? AF: 0.457 AC: 69475AN: 152124Hom.: 16510 Cov.: 33 AF XY: 0.455 AC XY: 33868AN XY: 74356
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ClinVar
Not reported inComputational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at