14-75449761-T-G

Position:

• chr14-75449761-T-G

Variant summary

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

The NM_001135048.2(JDP2):​c.201+11640T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,122 control chromosomes in the GnomAD database, including 45,161 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 0.77 (45161 hom., cov: 32)
• Consequence: JDP2 NM_001135048.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JDP2	NM_001135048.2	c.201+11640T>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.201+11640T>G		intron_variant			NM_001135048.2	ENSP00000498745.1

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116656 AN: 152004 Hom.: 45104 Cov.: 32

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.768 AC: 116779 AN: 152122 Hom.: 45161 Cov.: 32 AF XY: 0.772 AC XY: 57424 AN XY: 74352

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.729

Alfa AF: 0.722 Hom.: 51053

Bravo AF: 0.772

Asia WGS AF: 0.783 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.89
DANN	Benign	0.73

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: rs84044; hg19: chr14-75916464;