rs17149424
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022779.9(DDX31):c.588+174T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00744 in 674,100 control chromosomes in the GnomAD database, including 185 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 0.023 ( 136 hom., cov: 32)
Exomes 𝑓: 0.0030 ( 49 hom. )
Consequence
DDX31
NM_022779.9 intron
NM_022779.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.155
Genes affected
DDX31 (HGNC:16715): (DEAD-box helicase 31) DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a member of this family. The function of this member has not been determined. Alternative splicing of this gene generates multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2016]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0779 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX31 | NM_022779.9 | c.588+174T>G | intron_variant | ENST00000372159.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX31 | ENST00000372159.8 | c.588+174T>G | intron_variant | 1 | NM_022779.9 | P1 | |||
DDX31 | ENST00000480876.3 | c.589-139T>G | intron_variant | 1 | |||||
DDX31 | ENST00000310532.7 | c.588+174T>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0228 AC: 3469AN: 152060Hom.: 135 Cov.: 32
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GnomAD4 exome AF: 0.00295 AC: 1540AN: 521922Hom.: 49 AF XY: 0.00239 AC XY: 665AN XY: 277814
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GnomAD4 genome ? AF: 0.0228 AC: 3477AN: 152178Hom.: 136 Cov.: 32 AF XY: 0.0220 AC XY: 1639AN XY: 74406
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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