5-55739013-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_024415.3(DDX4):āc.50A>Gā(p.Tyr17Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000301 in 1,595,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024415.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDX4 | NM_024415.3 | c.50A>G | p.Tyr17Cys | missense_variant | 2/22 | ENST00000505374.6 | NP_077726.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDX4 | ENST00000505374.6 | c.50A>G | p.Tyr17Cys | missense_variant | 2/22 | 1 | NM_024415.3 | ENSP00000424838.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152028Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 250218Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135134
GnomAD4 exome AF: 0.0000284 AC: 41AN: 1443906Hom.: 0 Cov.: 27 AF XY: 0.0000292 AC XY: 21AN XY: 719406
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152028Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74236
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2021 | The c.50A>G (p.Y17C) alteration is located in exon 2 (coding exon 1) of the DDX4 gene. This alteration results from a A to G substitution at nucleotide position 50, causing the tyrosine (Y) at amino acid position 17 to be replaced by a cysteine (C). 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