Variant rs2229510 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BS1BS2

The NM_002229.3(JUNB):c.474C>A(p.Ser158=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0284 in 1,510,778 control chromosomes in the GnomAD database, including 731 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 0.021 ( 46 hom., cov: 32)

Exomes 𝑓: 0.029 ( 685 hom. )

Consequence

JUNB
NM_002229.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0990

Variant links:

Genes affected

JUNB (HGNC:6205): (JunB proto-oncogene, AP-1 transcription factor subunit) Enables sequence-specific double-stranded DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of transcription factor AP-1 complex. Biomarker of Hodgkin's lymphoma and anaplastic large cell lymphoma. [provided by Alliance of Genome Resources, Apr 2022]

JUNB links:

HOOK2 (HGNC:19885): (hook microtubule tethering protein 2) Hook proteins are cytosolic coiled-coil proteins that contain conserved N-terminal domains, which attach to microtubules, and more divergent C-terminal domains, which mediate binding to organelles. The Drosophila Hook protein is a component of the endocytic compartment.[supplied by OMIM, Apr 2004]

HOOK2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP7

Synonymous conserved (PhyloP=-0.099 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0215 (3269/152186) while in subpopulation NFE AF= 0.0356 (2420/67956). AF 95% confidence interval is 0.0344. There are 46 homozygotes in gnomad4. There are 1548 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 3269 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JUNB	NM_002229.3 linkuse as main transcript	c.474C>A	p.Ser158=	synonymous_variant	1/1	ENST00000302754.6
HOOK2	NM_001400043.1 linkuse as main transcript	c.-209+79G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
JUNB	ENST00000302754.6 linkuse as main transcript	c.474C>A	p.Ser158=	synonymous_variant	1/1		NM_002229.3	P1
HOOK2	ENST00000589765.1 linkuse as main transcript	n.42-18020G>T		intron_variant, non_coding_transcript_variant		5
HOOK2	ENST00000593143.5 linkuse as main transcript	n.259+79G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0215

AC:

3272

AN:

152068

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00579

Gnomad AMI

AF:

0.00549

Gnomad AMR

AF:

0.0116

Gnomad ASJ

AF:

0.00951

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00310

Gnomad FIN

AF:

0.0319

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0356

Gnomad OTH

AF:

0.0186

GnomAD3 exomes

AF:

0.0182

AC:

2132

AN:

116958

Hom.:

AF XY:

0.0181

AC XY:

1146

AN XY:

63436

show subpopulations

Gnomad AFR exome

AF:

0.00532

Gnomad AMR exome

AF:

0.00851

Gnomad ASJ exome

AF:

0.00840

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00377

Gnomad FIN exome

AF:

0.0329

Gnomad NFE exome

AF:

0.0310

Gnomad OTH exome

AF:

0.0189

GnomAD4 exome

AF:

0.0292

AC:

39630

AN:

1358592

Hom.:

685

Cov.:

AF XY:

0.0286

AC XY:

19068

AN XY:

666530

show subpopulations

Gnomad4 AFR exome

AF:

0.00429

Gnomad4 AMR exome

AF:

0.00812

Gnomad4 ASJ exome

AF:

0.00819

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00416

Gnomad4 FIN exome

AF:

0.0311

Gnomad4 NFE exome

AF:

0.0341

Gnomad4 OTH exome

AF:

0.0211

GnomAD4 genome

AF:

0.0215

AC:

3269

AN:

152186

Hom.:

Cov.:

AF XY:

0.0208

AC XY:

1548

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.00578

Gnomad4 AMR

AF:

0.0116

Gnomad4 ASJ

AF:

0.00951

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00311

Gnomad4 FIN

AF:

0.0319

Gnomad4 NFE

AF:

0.0356

Gnomad4 OTH

AF:

0.0184

Alfa

AF:

0.0237

Hom.:

Bravo

AF:

0.0187

Asia WGS

AF:

0.00346

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

7.2

DANN

Benign

0.91

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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