dbSNP rs8215: JDP2:c.*339T>C (chr14-75469814-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

8 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135048.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
JDP2	NM_001135048.2	MANE Select	c.*339T>C	3_prime_UTR	Exon 4 of 4	NP_001128520.1
JDP2	NM_001135049.1		c.*339T>C	3_prime_UTR	Exon 4 of 4	NP_001128521.1
JDP2	NM_001135047.2		c.*339T>C	3_prime_UTR	Exon 4 of 4	NP_001128519.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
JDP2	ENST00000651602.1	MANE Select	c.*339T>C	3_prime_UTR	Exon 4 of 4	ENSP00000498745.1
JDP2	ENST00000267569.5	TSL:1	c.*339T>C	3_prime_UTR	Exon 4 of 4	ENSP00000267569.5
JDP2	ENST00000435893.6	TSL:1	c.*339T>C	3_prime_UTR	Exon 4 of 4	ENSP00000399587.2

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

African (AFR)

AF:

0.330

AC:

631

AN:

1912

American (AMR)

AF:

0.423

AC:

902

AN:

2132

Ashkenazi Jewish (ASJ)

AF:

0.530

AC:

1180

AN:

2228

East Asian (EAS)

AF:

0.445

AC:

1753

AN:

3942

South Asian (SAS)

AF:

0.377

AC:

815

AN:

2162

European-Finnish (FIN)

AF:

0.524

AC:

1568

AN:

2992

Middle Eastern (MID)

AF:

0.500

AC:

136

AN:

272

European-Non Finnish (NFE)

AF:

0.513

AC:

17880

AN:

34830

Other (OTH)

AF:

0.491

AC:

1781

AN:

3624

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

644

1289

1933

2578

3222

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

224

336

448

560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.457

AC:

69475

AN:

152124

Hom.:

16510

Cov.:

AF XY:

0.455

AC XY:

33868

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.340

AC:

14102

AN:

41498

American (AMR)

AF:

0.432

AC:

6612

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.507

AC:

1762

AN:

3472

East Asian (EAS)

AF:

0.434

AC:

2237

AN:

5156

South Asian (SAS)

AF:

0.451

AC:

2178

AN:

4824

European-Finnish (FIN)

AF:

0.541

AC:

5725

AN:

10588

Middle Eastern (MID)

AF:

0.452

AC:

133

AN:

294

European-Non Finnish (NFE)

AF:

0.521

AC:

35390

AN:

67968

Other (OTH)

AF:

0.489

AC:

1033

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1951

3902

5852

7803

9754

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

636

1272

1908

2544

3180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.500

Hom.:

32065

Bravo

AF:

0.447

Asia WGS

AF:

0.431

AC:

1497

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.7

(source)

DANN

Benign

0.56

PhyloP100

0.040

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over