1-200644457-AATT-A
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP5
The NM_001031725.6(DDX59):c.1654_1656delAAT(p.Asn552del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.000000687 in 1,456,340 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
DDX59
NM_001031725.6 conservative_inframe_deletion
NM_001031725.6 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.97
Genes affected
DDX59 (HGNC:25360): (DEAD-box helicase 59) Predicted to enable RNA binding activity and RNA helicase activity. Predicted to be located in cytoplasm and nucleus. Predicted to be integral component of membrane. Implicated in orofaciodigital syndrome V. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_001031725.6. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 1-200644457-AATT-A is Pathogenic according to our data. Variant chr1-200644457-AATT-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 800916.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDX59 | NM_001031725.6 | c.1654_1656delAAT | p.Asn552del | conservative_inframe_deletion | 8/8 | ENST00000331314.11 | NP_001026895.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDX59 | ENST00000331314.11 | c.1654_1656delAAT | p.Asn552del | conservative_inframe_deletion | 8/8 | 1 | NM_001031725.6 | ENSP00000330460.6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456340Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 724444
GnomAD4 exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Orofaciodigital syndrome V Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City | Sep 26, 2019 | - - |
Computational scores
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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