rs199502364
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019070.5(DDX49):c.521C>A(p.Ala174Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000484 in 1,610,626 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A174V) has been classified as Uncertain significance.
Frequency
Consequence
NM_019070.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDX49 | NM_019070.5 | c.521C>A | p.Ala174Glu | missense_variant | Exon 5 of 13 | ENST00000247003.9 | NP_061943.2 | |
DDX49 | XM_011528084.4 | c.200C>A | p.Ala67Glu | missense_variant | Exon 6 of 14 | XP_011526386.1 | ||
DDX49 | NR_033677.2 | n.477C>A | non_coding_transcript_exon_variant | Exon 5 of 13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDX49 | ENST00000247003.9 | c.521C>A | p.Ala174Glu | missense_variant | Exon 5 of 13 | 1 | NM_019070.5 | ENSP00000247003.3 | ||
ENSG00000268193 | ENST00000596918.5 | n.*167+8926G>T | intron_variant | Intron 4 of 6 | 5 | ENSP00000469669.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000166 AC: 4AN: 240302Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131168
GnomAD4 exome AF: 0.0000514 AC: 75AN: 1458378Hom.: 0 Cov.: 33 AF XY: 0.0000469 AC XY: 34AN XY: 725456
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.521C>A (p.A174E) alteration is located in exon 5 (coding exon 5) of the DDX49 gene. This alteration results from a C to A substitution at nucleotide position 521, causing the alanine (A) at amino acid position 174 to be replaced by a glutamic acid (E). 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