chr1-111762955-TATG-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PM4_SupportingBP6_ModerateBS2
The NM_007204.5(DDX20):c.1268_1270del(p.Met423del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,613,950 control chromosomes in the GnomAD database, including 19 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0026 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0035 ( 18 hom. )
Consequence
DDX20
NM_007204.5 inframe_deletion
NM_007204.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.17
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 Likely_benign. Variant got -5 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_007204.5. Strenght limited to Supporting due to length of the change: 1aa.
BP6
?
Variant 1-111762955-TATG-T is Benign according to our data. Variant chr1-111762955-TATG-T is described in ClinVar as [Likely_benign]. Clinvar id is 2638995.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX20 | NM_007204.5 | c.1268_1270del | p.Met423del | inframe_deletion | 10/11 | ENST00000369702.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX20 | ENST00000369702.5 | c.1268_1270del | p.Met423del | inframe_deletion | 10/11 | 1 | NM_007204.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00261 AC: 397AN: 152062Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00235 AC: 590AN: 251430Hom.: 3 AF XY: 0.00249 AC XY: 339AN XY: 135882
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GnomAD4 exome AF: 0.00345 AC: 5048AN: 1461770Hom.: 18 AF XY: 0.00338 AC XY: 2459AN XY: 727186
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GnomAD4 genome ? AF: 0.00261 AC: 397AN: 152180Hom.: 1 Cov.: 32 AF XY: 0.00262 AC XY: 195AN XY: 74406
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | DDX20: BS2 - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at