14-75433818-A-G

Position:

• chr14-75433818-A-G

Variant summary

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

The NM_001135048.2(JDP2):​c.-23-4080A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,748 control chromosomes in the GnomAD database, including 13,079 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 0.39 (13079 hom., cov: 30)
• Consequence: JDP2 NM_001135048.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JDP2	NM_001135048.2	c.-23-4080A>G		intron_variant		ENST00000651602.1	NP_001128520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JDP2	ENST00000651602.1	c.-23-4080A>G		intron_variant			NM_001135048.2	ENSP00000498745	P1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59549 AN: 151628 Hom.: 13069 Cov.: 30

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.411

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.393 AC: 59568 AN: 151748 Hom.: 13079 Cov.: 30 AF XY: 0.394 AC XY: 29195 AN XY: 74124

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.409

Alfa AF: 0.440 Hom.: 6746

Bravo AF: 0.379

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs715463; hg19: chr14-75900521;