Variant chr6-31539077-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_004640.7(DDX39B):c.339+70G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 1,612,668 control chromosomes in the GnomAD database, including 554,719 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 0.85 ( 54736 hom., cov: 31)

Exomes 𝑓: 0.83 ( 499983 hom. )

Consequence

DDX39B
NM_004640.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.799

Variant links:

Genes affected

DDX39B (HGNC:13917): (DExD-box helicase 39B) This gene encodes a member of the DEAD box family of RNA-dependent ATPases that mediate ATP hydrolysis during pre-mRNA splicing. The encoded protein is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. This gene belongs to a cluster of genes localized in the vicinity of the genes encoding tumor necrosis factor alpha and tumor necrosis factor beta. These genes are all within the human major histocompatibility complex class III region. Mutations in this gene may be associated with rheumatoid arthritis. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on both chromosomes 6 and 11. Read-through transcription also occurs between this gene and the upstream ATP6V1G2 (ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2) gene. [provided by RefSeq, Feb 2011]

DDX39B links:

ATP6V1G2-DDX39B (HGNC:):

ATP6V1G2-DDX39B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
DDX39B	NM_004640.7 linkuse as main transcript	c.339+70G>A	intron_variant	ENST00000396172.6
ATP6V1G2-DDX39B	NR_037853.1 linkuse as main transcript	n.1142+70G>A	intron_variant, non_coding_transcript_variant
DDX39B	NM_080598.6 linkuse as main transcript	c.339+70G>A	intron_variant
DDX39B	NR_037852.2 linkuse as main transcript	n.397+1245G>A	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDX39B	ENST00000396172.6 linkuse as main transcript	c.339+70G>A		intron_variant		1	NM_004640.7	P1	Q13838-1

Frequencies

GnomAD3 genomes

AF:

0.847

AC:

128802

AN:

152010

Hom.:

54679

Cov.:

show subpopulations

Gnomad AFR

AF:

0.876

Gnomad AMI

AF:

0.826

Gnomad AMR

AF:

0.868

Gnomad ASJ

AF:

0.940

Gnomad EAS

AF:

0.926

Gnomad SAS

AF:

0.923

Gnomad FIN

AF:

0.824

Gnomad MID

AF:

0.908

Gnomad NFE

AF:

0.813

Gnomad OTH

AF:

0.860

GnomAD3 exomes

AF:

0.856

AC:

211598

AN:

247256

Hom.:

90962

AF XY:

0.861

AC XY:

115833

AN XY:

134582

show subpopulations

Gnomad AFR exome

AF:

0.873

Gnomad AMR exome

AF:

0.857

Gnomad ASJ exome

AF:

0.944

Gnomad EAS exome

AF:

0.932

Gnomad SAS exome

AF:

0.925

Gnomad FIN exome

AF:

0.817

Gnomad NFE exome

AF:

0.821

Gnomad OTH exome

AF:

0.853

GnomAD4 exome

AF:

0.826

AC:

1206696

AN:

1460540

Hom.:

499983

Cov.:

AF XY:

0.830

AC XY:

603321

AN XY:

726612

show subpopulations

Gnomad4 AFR exome

AF:

0.883

Gnomad4 AMR exome

AF:

0.865

Gnomad4 ASJ exome

AF:

0.940

Gnomad4 EAS exome

AF:

0.920

Gnomad4 SAS exome

AF:

0.926

Gnomad4 FIN exome

AF:

0.816

Gnomad4 NFE exome

AF:

0.809

Gnomad4 OTH exome

AF:

0.836

GnomAD4 genome

AF:

0.847

AC:

128917

AN:

152128

Hom.:

54736

Cov.:

AF XY:

0.852

AC XY:

63332

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.876

Gnomad4 AMR

AF:

0.868

Gnomad4 ASJ

AF:

0.940

Gnomad4 EAS

AF:

0.926

Gnomad4 SAS

AF:

0.923

Gnomad4 FIN

AF:

0.824

Gnomad4 NFE

AF:

0.813

Gnomad4 OTH

AF:

0.861

Alfa

AF:

0.833

Hom.:

40556

Bravo

AF:

0.851

Asia WGS

AF:

0.865

AC:

3011

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

9.3

DANN

Benign

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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