14-75456963-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001135048.2(JDP2):​c.202-4463T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,102 control chromosomes in the GnomAD database, including 43,968 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 0.76 ( 43968 hom., cov: 32)

Consequence

JDP2
NM_001135048.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.511
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
JDP2NM_001135048.2 linkc.202-4463T>C intron_variant Intron 2 of 3 ENST00000651602.1 NP_001128520.1 Q8WYK2-1A0A024R6D7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
JDP2ENST00000651602.1 linkc.202-4463T>C intron_variant Intron 2 of 3 NM_001135048.2 ENSP00000498745.1 Q8WYK2-1

Frequencies

GnomAD3 genomes
AF:
0.758
AC:
115266
AN:
151984
Hom.:
43939
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.818
Gnomad AMI
AF:
0.542
Gnomad AMR
AF:
0.701
Gnomad ASJ
AF:
0.775
Gnomad EAS
AF:
0.730
Gnomad SAS
AF:
0.729
Gnomad FIN
AF:
0.715
Gnomad MID
AF:
0.748
Gnomad NFE
AF:
0.748
Gnomad OTH
AF:
0.752
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.758
AC:
115348
AN:
152102
Hom.:
43968
Cov.:
32
AF XY:
0.752
AC XY:
55908
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.818
Gnomad4 AMR
AF:
0.701
Gnomad4 ASJ
AF:
0.775
Gnomad4 EAS
AF:
0.729
Gnomad4 SAS
AF:
0.728
Gnomad4 FIN
AF:
0.715
Gnomad4 NFE
AF:
0.748
Gnomad4 OTH
AF:
0.749
Alfa
AF:
0.745
Hom.:
59905
Bravo
AF:
0.761
Asia WGS
AF:
0.724
AC:
2518
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.9
DANN
Benign
0.72

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs175646; hg19: chr14-75923666; API