17-5450388-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020162.4(DHX33):āc.1543A>Gā(p.Lys515Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000954 in 1,614,102 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 (ā ).
Frequency
Consequence
NM_020162.4 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DHX33 | NM_020162.4 | c.1543A>G | p.Lys515Glu | missense_variant | 10/12 | ENST00000225296.8 | NP_064547.2 | |
DHX33 | NM_001199699.2 | c.1024A>G | p.Lys342Glu | missense_variant | 9/11 | NP_001186628.1 | ||
DHX33 | XM_047436418.1 | c.1415A>G | p.Gln472Arg | missense_variant | 9/9 | XP_047292374.1 | ||
DHX33 | XM_017024877.2 | c.259A>G | p.Lys87Glu | missense_variant | 6/8 | XP_016880366.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000467 AC: 71AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000115 AC: 29AN: 251272Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135820
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461802Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727184
GnomAD4 genome AF: 0.000473 AC: 72AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2024 | The c.1543A>G (p.K515E) alteration is located in exon 10 (coding exon 10) of the DHX33 gene. This alteration results from a A to G substitution at nucleotide position 1543, causing the lysine (K) at amino acid position 515 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