10-68901404-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024045.2(DDX50):āc.20G>Cā(p.Trp7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000242 in 1,566,678 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024045.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDX50 | NM_024045.2 | c.20G>C | p.Trp7Ser | missense_variant | 1/15 | ENST00000373585.8 | NP_076950.1 | |
DDX50 | XM_011540144.3 | c.-230G>C | 5_prime_UTR_variant | 1/16 | XP_011538446.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDX50 | ENST00000373585.8 | c.20G>C | p.Trp7Ser | missense_variant | 1/15 | 1 | NM_024045.2 | ENSP00000362687.3 | ||
DDX50 | ENST00000471475.1 | n.20G>C | non_coding_transcript_exon_variant | 1/6 | 5 | ENSP00000474314.1 | ||||
DDX50 | ENST00000483593.5 | n.20G>C | non_coding_transcript_exon_variant | 1/7 | 3 | ENSP00000474785.1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000185 AC: 33AN: 178216Hom.: 0 AF XY: 0.000168 AC XY: 16AN XY: 95300
GnomAD4 exome AF: 0.000252 AC: 357AN: 1414442Hom.: 1 Cov.: 30 AF XY: 0.000259 AC XY: 181AN XY: 699586
GnomAD4 genome AF: 0.000145 AC: 22AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 10, 2024 | The c.20G>C (p.W7S) alteration is located in exon 1 (coding exon 1) of the DDX50 gene. This alteration results from a G to C substitution at nucleotide position 20, causing the tryptophan (W) at amino acid position 7 to be replaced by a serine (S). 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