rs2523512
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004640.7(DDX39B):c.339+123C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,555,856 control chromosomes in the GnomAD database, including 23,220 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 0.16 ( 2146 hom., cov: 33)
Exomes 𝑓: 0.17 ( 21074 hom. )
Consequence
DDX39B
NM_004640.7 intron
NM_004640.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0880
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 (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDX39B | NM_004640.7 | c.339+123C>T | intron_variant | ENST00000396172.6 | NP_004631.1 | |||
ATP6V1G2-DDX39B | NR_037853.1 | n.1142+123C>T | intron_variant, non_coding_transcript_variant | |||||
DDX39B | NM_080598.6 | c.339+123C>T | intron_variant | NP_542165.1 | ||||
DDX39B | NR_037852.2 | n.397+1298C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDX39B | ENST00000396172.6 | c.339+123C>T | intron_variant | 1 | NM_004640.7 | ENSP00000379475 | P1 |
Frequencies
GnomAD3 genomes AF: 0.165 AC: 25031AN: 152046Hom.: 2147 Cov.: 33
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GnomAD3 exomes AF: 0.180 AC: 44599AN: 247838Hom.: 4235 AF XY: 0.187 AC XY: 25136AN XY: 134570
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GnomAD4 exome AF: 0.170 AC: 238585AN: 1403692Hom.: 21074 Cov.: 27 AF XY: 0.174 AC XY: 121935AN XY: 701554
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GnomAD4 genome AF: 0.165 AC: 25048AN: 152164Hom.: 2146 Cov.: 33 AF XY: 0.165 AC XY: 12304AN XY: 74362
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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