17-5450232-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_020162.4(DHX33):c.1699C>T(p.Arg567Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,614,064 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic 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. R567Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_020162.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHX33 | NM_020162.4 | c.1699C>T | p.Arg567Trp | missense_variant | 10/12 | ENST00000225296.8 | |
DHX33 | NM_001199699.2 | c.1180C>T | p.Arg394Trp | missense_variant | 9/11 | ||
DHX33 | XM_047436418.1 | c.1571C>T | p.Ser524Leu | missense_variant | 9/9 | ||
DHX33 | XM_017024877.2 | c.415C>T | p.Arg139Trp | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHX33 | ENST00000225296.8 | c.1699C>T | p.Arg567Trp | missense_variant | 10/12 | 1 | NM_020162.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251490Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135920
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461878Hom.: 1 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727236
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.1699C>T (p.R567W) alteration is located in exon 10 (coding exon 10) of the DHX33 gene. This alteration results from a C to T substitution at nucleotide position 1699, causing the arginine (R) at amino acid position 567 to be replaced by a tryptophan (W). 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