14-75469814-T-C

Position:

• chr14-75469814-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

ACMG classification

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: 69472 AN: 152006 Hom.: 16509 Cov.: 33

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.: 0 AF XY: 0.495 AC XY: 13718 AN XY: 27732

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.: 33 AF XY: 0.455 AC XY: 33868 AN XY: 74356

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

Other links and lift over

dbSNP: rs8215; hg19: chr14-75936517; COSMIC: COSV50868112; COSMIC: COSV50868112;