rs9281523
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_004640.7(DDX39B):c.1271-18_1271-17insG variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,612,418 control chromosomes in the GnomAD database, including 11,986 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.099 ( 857 hom., cov: 29)
Exomes 𝑓: 0.11 ( 11129 hom. )
Consequence
DDX39B
NM_004640.7 splice_polypyrimidine_tract, intron
NM_004640.7 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.396
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 -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX39B | NM_004640.7 | c.1271-18_1271-17insG | splice_polypyrimidine_tract_variant, intron_variant | ENST00000396172.6 | |||
ATP6V1G2-DDX39B | NR_037853.1 | n.2074-18_2074-17insG | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
DDX39B | NM_080598.6 | c.1271-18_1271-17insG | splice_polypyrimidine_tract_variant, intron_variant | ||||
DDX39B | NR_037852.2 | n.1236-18_1236-17insG | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX39B | ENST00000396172.6 | c.1271-18_1271-17insG | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004640.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0994 AC: 15107AN: 151992Hom.: 855 Cov.: 29
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GnomAD3 exomes AF: 0.0813 AC: 20014AN: 246126Hom.: 1077 AF XY: 0.0800 AC XY: 10729AN XY: 134168
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GnomAD4 exome AF: 0.114 AC: 166961AN: 1460308Hom.: 11129 Cov.: 33 AF XY: 0.112 AC XY: 81109AN XY: 726490
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GnomAD4 genome ? AF: 0.0994 AC: 15113AN: 152110Hom.: 857 Cov.: 29 AF XY: 0.0947 AC XY: 7042AN XY: 74374
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ClinVar
Not reported inComputational scores
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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