1-200644311-T-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001031725.6(DDX59):āc.1803A>Cā(p.Thr601=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,613,254 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000053 ( 0 hom., cov: 32)
Exomes š: 0.000021 ( 0 hom. )
Consequence
DDX59
NM_001031725.6 synonymous
NM_001031725.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.30
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 1-200644311-T-G is Benign according to our data. Variant chr1-200644311-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 3026097.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX59 | NM_001031725.6 | c.1803A>C | p.Thr601= | synonymous_variant | 8/8 | ENST00000331314.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX59 | ENST00000331314.11 | c.1803A>C | p.Thr601= | synonymous_variant | 8/8 | 1 | NM_001031725.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250536Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135432
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GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461036Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726790
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74364
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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 | Feb 01, 2024 | DDX59: BP4, BP7 - |
Computational scores
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CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at