rs741846

Variant names:

• chr14-75451512-G-A
• rs741846
• NM_001135048.2:c.202-9914G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JDP2	NM_001135048.2	MANE Select	c.202-9914G>A		intron	N/A	NP_001128520.1
	JDP2	NM_001135049.1		c.235-9914G>A		intron	N/A	NP_001128521.1
	JDP2	NM_001135047.2		c.202-9914G>A		intron	N/A	NP_001128519.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JDP2	ENST00000651602.1	MANE Select	c.202-9914G>A		intron	N/A	ENSP00000498745.1
	JDP2	ENST00000267569.5	TSL:1	c.235-9914G>A		intron	N/A	ENSP00000267569.5
	JDP2	ENST00000435893.6	TSL:1	c.202-9914G>A		intron	N/A	ENSP00000399587.2

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

African (AFR) AF: 0.0852 AC: 3539 AN: 41528

American (AMR) AF: 0.287 AC: 4390 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2303 AN: 5164

South Asian (SAS) AF: 0.344 AC: 1658 AN: 4814

European-Finnish (FIN) AF: 0.359 AC: 3783 AN: 10550

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22178 AN: 67962

Other (OTH) AF: 0.264 AC: 556 AN: 2106

Alfa AF: 0.296 Hom.: 11194

Bravo AF: 0.249

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.79
PhyloP100		-0.73
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs741846; hg19: chr14-75918215;