dbSNP rs2999131: JUN-DT:n.153+46841G>C (chr1-58832146-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000419531.3(JUN-DT):n.153+46841G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,092 control chromosomes in the GnomAD database, including 14,093 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 0.41 ( 14093 hom., cov: 32)

Consequence

JUN-DT
ENST00000419531.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.882

Publications

0 publications found

Variant links:

Genes affected

JUN-DT (HGNC:49450): (JUN divergent transcript)

JUN-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
JUN-DT	NR_034014.1 link	n.155+46841G>C	intron_variant	Intron 1 of 3
JUN-DT	NR_034015.1 link	n.155+46841G>C	intron_variant	Intron 1 of 2
JUN-DT	NR_108106.1 link	n.155+46841G>C	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
JUN-DT	ENST00000419531.3 link	n.153+46841G>C	intron_variant	Intron 1 of 3	4
JUN-DT	ENST00000649834.1 link	n.178+46841G>C	intron_variant	Intron 1 of 2
JUN-DT	ENST00000653297.1 link	n.178+46841G>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.407

AC:

61873

AN:

151972

Hom.:

14062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.619

Gnomad AMI

AF:

0.253

Gnomad AMR

AF:

0.411

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.222

Gnomad SAS

AF:

0.282

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.335

Gnomad OTH

AF:

0.387

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

GnomAD4 genome

AF:

0.407

AC:

61964

AN:

152092

Hom.:

14093

Cov.:

AF XY:

0.399

AC XY:

29659

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.619

AC:

25665

AN:

41470

American (AMR)

AF:

0.411

AC:

6276

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.352

AC:

1220

AN:

3468

East Asian (EAS)

AF:

0.222

AC:

1151

AN:

5182

South Asian (SAS)

AF:

0.282

AC:

1362

AN:

4822

European-Finnish (FIN)

AF:

0.224

AC:

2367

AN:

10572

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.335

AC:

22764

AN:

67994

Other (OTH)

AF:

0.388

AC:

818

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1747

3493

5240

6986

8733

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.373

Hom.:

1462

Bravo

AF:

0.430

Asia WGS

AF:

0.293

AC:

1024

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.16

(source)

DANN

Benign

0.39

PhyloP100

-0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs2999131

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over