rs28372907
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020162.4(DHX33):c.-80C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 1,428,252 control chromosomes in the GnomAD database, including 39,530 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.29 ( 7773 hom., cov: 32)
Exomes 𝑓: 0.21 ( 31757 hom. )
Consequence
DHX33
NM_020162.4 5_prime_UTR
NM_020162.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.27
Genes affected
DHX33 (HGNC:16718): (DEAH-box helicase 33) This gene encodes a member of the DEAD box protein family. The DEAD box proteins are characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DHX33 | NM_020162.4 | c.-80C>T | 5_prime_UTR_variant | 1/12 | ENST00000225296.8 | NP_064547.2 | ||
DHX33 | NM_001199699.2 | c.-438C>T | 5_prime_UTR_variant | 1/11 | NP_001186628.1 | |||
DHX33 | XM_047436418.1 | c.-80C>T | 5_prime_UTR_variant | 1/9 | XP_047292374.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DHX33 | ENST00000225296.8 | c.-80C>T | 5_prime_UTR_variant | 1/12 | 1 | NM_020162.4 | ENSP00000225296.3 | |||
DHX33 | ENST00000433302.7 | c.-80C>T | upstream_gene_variant | 1 | ENSP00000413779.3 |
Frequencies
GnomAD3 genomes AF: 0.289 AC: 43821AN: 151858Hom.: 7716 Cov.: 32
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GnomAD3 exomes AF: 0.237 AC: 26366AN: 111224Hom.: 3441 AF XY: 0.243 AC XY: 15134AN XY: 62202
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GnomAD4 exome AF: 0.213 AC: 271338AN: 1276276Hom.: 31757 Cov.: 19 AF XY: 0.215 AC XY: 136396AN XY: 634814
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GnomAD4 genome AF: 0.289 AC: 43935AN: 151976Hom.: 7773 Cov.: 32 AF XY: 0.289 AC XY: 21474AN XY: 74292
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at