6-30660305-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003587.5(DHX16):c.1545-63T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 1,340,388 control chromosomes in the GnomAD database, including 571,334 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 0.94 ( 67708 hom., cov: 31)
Exomes 𝑓: 0.92 ( 503626 hom. )
Consequence
DHX16
NM_003587.5 intron
NM_003587.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.286
Genes affected
DHX16 (HGNC:2739): (DEAH-box helicase 16) DEAD box proteins, 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 family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is a functional homolog of fission yeast Prp8 protein involved in cell cycle progression. This gene is mapped to the MHC region on chromosome 6p21.3, a region where many malignant, genetic and autoimmune disease genes are linked. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2018]
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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=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DHX16 | NM_003587.5 | c.1545-63T>C | intron_variant | ENST00000376442.8 | NP_003578.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DHX16 | ENST00000376442.8 | c.1545-63T>C | intron_variant | 1 | NM_003587.5 | ENSP00000365625.3 | ||||
DHX16 | ENST00000376437.9 | c.102-63T>C | intron_variant | 1 | ENSP00000365620.5 | |||||
DHX16 | ENST00000480966.1 | n.273T>C | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.942 AC: 143356AN: 152144Hom.: 67651 Cov.: 31
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GnomAD4 exome AF: 0.920 AC: 1093415AN: 1188126Hom.: 503626 Cov.: 15 AF XY: 0.922 AC XY: 538842AN XY: 584408
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GnomAD4 genome AF: 0.942 AC: 143472AN: 152262Hom.: 67708 Cov.: 31 AF XY: 0.943 AC XY: 70160AN XY: 74428
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at