rs741846

Positions:

• chr14-75451512-G-A
• chr14-75451512-G-T

Variant summary

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

The NM_001135048.2(JDP2):​c.202-9914G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,092 control chromosomes in the GnomAD database, including 6,135 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 0.26 (6135 hom., cov: 31)
• Consequence: JDP2 NM_001135048.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JDP2	NM_001135048.2	c.202-9914G>A		intron_variant		ENST00000651602.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JDP2	ENST00000651602.1	c.202-9914G>A		intron_variant			NM_001135048.2	P1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39451 AN: 151974 Hom.: 6139 Cov.: 31

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.259 AC: 39451 AN: 152092 Hom.: 6135 Cov.: 31 AF XY: 0.262 AC XY: 19486 AN XY: 74330

Gnomad4 AFR AF: 0.0852

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.264

Alfa AF: 0.300 Hom.: 8093

Bravo AF: 0.249

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.79

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: rs741846; hg19: chr14-75918215;