rs2071596
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004640.7(DDX39B):c.340-59C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 1,563,490 control chromosomes in the GnomAD database, including 27,338 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 0.22 ( 3928 hom., cov: 32)
Exomes 𝑓: 0.17 ( 23410 hom. )
Consequence
DDX39B
NM_004640.7 intron
NM_004640.7 intron
Scores
1
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.24
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]
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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 (MetaRNN=0.0035931468).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX39B | NM_004640.7 | c.340-59C>T | intron_variant | ENST00000396172.6 | |||
ATP6V1G2-DDX39B | NR_037853.1 | n.1143-59C>T | intron_variant, non_coding_transcript_variant | ||||
DDX39B | NM_080598.6 | c.340-59C>T | intron_variant | ||||
DDX39B | NR_037852.2 | n.397+1408C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX39B | ENST00000396172.6 | c.340-59C>T | intron_variant | 1 | NM_004640.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.218 AC: 33047AN: 151862Hom.: 3929 Cov.: 32
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GnomAD3 exomes AF: 0.203 AC: 50782AN: 250300Hom.: 5729 AF XY: 0.192 AC XY: 26001AN XY: 135296
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GnomAD4 exome AF: 0.175 AC: 246668AN: 1411508Hom.: 23410 Cov.: 26 AF XY: 0.171 AC XY: 120885AN XY: 705202
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GnomAD4 genome ? AF: 0.218 AC: 33077AN: 151982Hom.: 3928 Cov.: 32 AF XY: 0.218 AC XY: 16187AN XY: 74270
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647
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689
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24352
Asia WGS
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795
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P;P;P
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;D
Sift4G
Uncertain
D;.
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at