Variant rs8215 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0400

Variant links:

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]

JDP2 links:

Genome browser will be placed here

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 linkuse as main transcript	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 linkuse as main transcript	c.*339T>C		3_prime_UTR_variant	4/4		NM_001135048.2	P1	Q8WYK2-1

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69472

AN:

152006

Hom.:

16509

Cov.:

show subpopulations

Gnomad AFR

AF:

0.340

Gnomad AMI

AF:

0.334

Gnomad AMR

AF:

0.432

Gnomad ASJ

AF:

0.507

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.453

Gnomad FIN

AF:

0.541

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.491

GnomAD4 exome

AF:

0.493

AC:

26646

AN:

54094

Hom.:

6855

Cov.:

AF XY:

0.495

AC XY:

13718

AN XY:

27732

show subpopulations

Gnomad4 AFR exome

AF:

0.330

Gnomad4 AMR exome

AF:

0.423

Gnomad4 ASJ exome

AF:

0.530

Gnomad4 EAS exome

AF:

0.445

Gnomad4 SAS exome

AF:

0.377

Gnomad4 FIN exome

AF:

0.524

Gnomad4 NFE exome

AF:

0.513

Gnomad4 OTH exome

AF:

0.491

GnomAD4 genome

AF:

0.457

AC:

69475

AN:

152124

Hom.:

16510

Cov.:

AF XY:

0.455

AC XY:

33868

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.340

Gnomad4 AMR

AF:

0.432

Gnomad4 ASJ

AF:

0.507

Gnomad4 EAS

AF:

0.434

Gnomad4 SAS

AF:

0.451

Gnomad4 FIN

AF:

0.541

Gnomad4 NFE

AF:

0.521

Gnomad4 OTH

AF:

0.489

Alfa

AF:

0.505

Hom.:

25751

Bravo

AF:

0.447

Asia WGS

AF:

0.431

AC:

1497

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.7

DANN

Benign

0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over