rs197413
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_007204.5(DDX20):c.1926G>A(p.Val642=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 1,613,552 control chromosomes in the GnomAD database, including 140,356 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 0.48 ( 19098 hom., cov: 32)
Exomes 𝑓: 0.40 ( 121258 hom. )
Consequence
DDX20
NM_007204.5 synonymous
NM_007204.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.15
Genes affected
DDX20 (HGNC:2743): (DEAD-box helicase 20) 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 family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which has an ATPase activity and is a component of the survival of motor neurons (SMN) complex. This protein interacts directly with SMN, the spinal muscular atrophy gene product, and may play a catalytic role in the function of the SMN complex on RNPs. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP7
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Synonymous conserved (PhyloP=-1.14 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX20 | NM_007204.5 | c.1926G>A | p.Val642= | synonymous_variant | 11/11 | ENST00000369702.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX20 | ENST00000369702.5 | c.1926G>A | p.Val642= | synonymous_variant | 11/11 | 1 | NM_007204.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.483 AC: 73388AN: 151986Hom.: 19056 Cov.: 32
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GnomAD3 exomes AF: 0.427 AC: 107035AN: 250932Hom.: 23926 AF XY: 0.413 AC XY: 56094AN XY: 135658
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GnomAD4 exome AF: 0.402 AC: 587501AN: 1461446Hom.: 121258 Cov.: 49 AF XY: 0.399 AC XY: 289990AN XY: 727038
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GnomAD4 genome ? AF: 0.483 AC: 73498AN: 152106Hom.: 19098 Cov.: 32 AF XY: 0.480 AC XY: 35657AN XY: 74336
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at