Variant rs11688 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002228.4(JUN):c.750G>A(p.Gln250=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0577 in 1,614,190 control chromosomes in the GnomAD database, including 3,798 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 0.093 ( 1064 hom., cov: 32)

Exomes 𝑓: 0.054 ( 2734 hom. )

Consequence

JUN
NM_002228.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.73

Variant links:

Genes affected

JUN (HGNC:6204): (Jun proto-oncogene, AP-1 transcription factor subunit) This gene is the putative transforming gene of avian sarcoma virus 17. It encodes a protein which is highly similar to the viral protein, and which interacts directly with specific target DNA sequences to regulate gene expression. This gene is intronless and is mapped to 1p32-p31, a chromosomal region involved in both translocations and deletions in human malignancies. [provided by RefSeq, Jul 2008]

JUN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP7

Synonymous conserved (PhyloP=1.73 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JUN	NM_002228.4 linkuse as main transcript	c.750G>A	p.Gln250=	synonymous_variant	1/1	ENST00000371222.4	NP_002219.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	Appris
JUN	ENST00000371222.4 linkuse as main transcript	c.750G>A	p.Gln250=	synonymous_variant	1/1	NM_002228.4	ENSP00000360266	P1
JUN	ENST00000710273.1 linkuse as main transcript	c.816G>A	p.Gln272=	synonymous_variant	1/1		ENSP00000518166
JUN	ENST00000678696.1 linkuse as main transcript	c.750G>A	p.Gln250=	synonymous_variant, NMD_transcript_variant	1/4		ENSP00000503132

Frequencies

GnomAD3 genomes

AF:

0.0930

AC:

14146

AN:

152186

Hom.:

1062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.0578

Gnomad ASJ

AF:

0.0136

Gnomad EAS

AF:

0.0208

Gnomad SAS

AF:

0.0161

Gnomad FIN

AF:

0.0499

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0538

Gnomad OTH

AF:

0.0788

GnomAD3 exomes

AF:

0.0528

AC:

13268

AN:

251158

Hom.:

630

AF XY:

0.0495

AC XY:

6723

AN XY:

135862

show subpopulations

Gnomad AFR exome

AF:

0.214

Gnomad AMR exome

AF:

0.0324

Gnomad ASJ exome

AF:

0.0183

Gnomad EAS exome

AF:

0.0284

Gnomad SAS exome

AF:

0.0183

Gnomad FIN exome

AF:

0.0471

Gnomad NFE exome

AF:

0.0537

Gnomad OTH exome

AF:

0.0518

GnomAD4 exome

AF:

0.0540

AC:

78897

AN:

1461886

Hom.:

2734

Cov.:

AF XY:

0.0523

AC XY:

38040

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.216

Gnomad4 AMR exome

AF:

0.0345

Gnomad4 ASJ exome

AF:

0.0176

Gnomad4 EAS exome

AF:

0.0221

Gnomad4 SAS exome

AF:

0.0185

Gnomad4 FIN exome

AF:

0.0483

Gnomad4 NFE exome

AF:

0.0550

Gnomad4 OTH exome

AF:

0.0539

GnomAD4 genome

AF:

0.0931

AC:

14172

AN:

152304

Hom.:

1064

Cov.:

AF XY:

0.0907

AC XY:

6755

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.208

Gnomad4 AMR

AF:

0.0578

Gnomad4 ASJ

AF:

0.0136

Gnomad4 EAS

AF:

0.0208

Gnomad4 SAS

AF:

0.0159

Gnomad4 FIN

AF:

0.0499

Gnomad4 NFE

AF:

0.0538

Gnomad4 OTH

AF:

0.0780

Alfa

AF:

0.0582

Hom.:

553

Bravo

AF:

0.0981

Asia WGS

AF:

0.0360

AC:

126

AN:

3478

EpiCase

AF:

0.0485

EpiControl

AF:

0.0483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

9.1

DANN

Benign

0.97

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over