chr17-63812206-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PP2PP3_Moderate
The NM_203499.3(DDX42):c.1673C>T(p.Ala558Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000412 in 1,457,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_203499.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX42 | NM_203499.3 | c.1673C>T | p.Ala558Val | missense_variant, splice_region_variant | 14/18 | ENST00000389924.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX42 | ENST00000389924.7 | c.1673C>T | p.Ala558Val | missense_variant, splice_region_variant | 14/18 | 5 | NM_203499.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249056Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134786
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1457900Hom.: 0 Cov.: 32 AF XY: 0.00000414 AC XY: 3AN XY: 724900
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2023 | The c.1673C>T (p.A558V) alteration is located in exon 15 (coding exon 13) of the DDX42 gene. This alteration results from a C to T substitution at nucleotide position 1673, causing the alanine (A) at amino acid position 558 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at