chr6-31538871-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004640.7(DDX39B):c.340-16C>A 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 0.749 in 1,610,388 control chromosomes in the GnomAD database, including 453,136 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
Consequence
NM_004640.7 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX39B | NM_004640.7 | c.340-16C>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000396172.6 | |||
ATP6V1G2-DDX39B | NR_037853.1 | n.1143-16C>A | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
DDX39B | NM_080598.6 | c.340-16C>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
DDX39B | NR_037852.2 | n.397+1451C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX39B | ENST00000396172.6 | c.340-16C>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004640.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.762 AC: 115839AN: 151922Hom.: 44530 Cov.: 32
GnomAD3 exomes AF: 0.758 AC: 190486AN: 251372Hom.: 72778 AF XY: 0.757 AC XY: 102874AN XY: 135850
GnomAD4 exome AF: 0.747 AC: 1089622AN: 1458348Hom.: 408559 Cov.: 39 AF XY: 0.748 AC XY: 542629AN XY: 725660
GnomAD4 genome AF: 0.763 AC: 115945AN: 152040Hom.: 44577 Cov.: 32 AF XY: 0.757 AC XY: 56225AN XY: 74314
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at