chr5-55792682-T-G
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_024415.3(DDX4):āc.1344T>Gā(p.Ala448=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00051 in 1,597,380 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0029 ( 4 hom., cov: 32)
Exomes š: 0.00025 ( 2 hom. )
Consequence
DDX4
NM_024415.3 synonymous
NM_024415.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.840
Genes affected
DDX4 (HGNC:18700): (DEAD-box helicase 4) 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 is a homolog of VASA proteins in Drosophila and several other species. The gene is specifically expressed in the germ cell lineage in both sexes and functions in germ cell development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 5-55792682-T-G is Benign according to our data. Variant chr5-55792682-T-G is described in ClinVar as [Benign]. Clinvar id is 726743.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.84 with no splicing effect.
BS2
High AC in GnomAd4 at 449 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX4 | NM_024415.3 | c.1344T>G | p.Ala448= | synonymous_variant | 17/22 | ENST00000505374.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX4 | ENST00000505374.6 | c.1344T>G | p.Ala448= | synonymous_variant | 17/22 | 1 | NM_024415.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00294 AC: 448AN: 152158Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.000779 AC: 189AN: 242516Hom.: 0 AF XY: 0.000579 AC XY: 76AN XY: 131346
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GnomAD4 exome AF: 0.000253 AC: 366AN: 1445104Hom.: 2 Cov.: 29 AF XY: 0.000221 AC XY: 159AN XY: 718898
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GnomAD4 genome AF: 0.00295 AC: 449AN: 152276Hom.: 4 Cov.: 32 AF XY: 0.00283 AC XY: 211AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2018 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at