16-72096241-G-A
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_ModerateBP6_Very_Strong
The ENST00000268482.8(DHX38):c.84G>A(p.Lys28=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000275 in 1,614,174 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00089 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 1 hom. )
Consequence
DHX38
ENST00000268482.8 synonymous
ENST00000268482.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.83
Genes affected
DHX38 (HGNC:17211): (DEAH-box helicase 38) 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. The protein encoded by this gene is a member of the DEAD/H box family of splicing factors. This protein resembles yeast Prp16 more closely than other DEAD/H family members. It is an ATPase and essential for the catalytic step II in pre-mRNA splicing process. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BP6
Variant 16-72096241-G-A is Benign according to our data. Variant chr16-72096241-G-A is described in ClinVar as [Benign]. Clinvar id is 1169701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-72096241-G-A is described in Lovd as [Benign]. Variant chr16-72096241-G-A is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
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DHX38 | NM_014003.4 | c.84G>A | p.Lys28= | synonymous_variant | 2/27 | ENST00000268482.8 | NP_054722.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DHX38 | ENST00000268482.8 | c.84G>A | p.Lys28= | synonymous_variant | 2/27 | 1 | NM_014003.4 | ENSP00000268482 | P1 | |
DHX38 | ENST00000566794.5 | c.84G>A | p.Lys28= | synonymous_variant | 2/3 | 4 | ENSP00000455939 | |||
DHX38 | ENST00000566489.1 | c.84G>A | p.Lys28= | synonymous_variant | 3/4 | 4 | ENSP00000457887 | |||
DHX38 | ENST00000579387.5 | c.84G>A | p.Lys28= | synonymous_variant, NMD_transcript_variant | 2/12 | 5 | ENSP00000462149 |
Frequencies
GnomAD3 genomes AF: 0.000894 AC: 136AN: 152198Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000358 AC: 90AN: 251364Hom.: 1 AF XY: 0.000324 AC XY: 44AN XY: 135880
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GnomAD4 exome AF: 0.000211 AC: 308AN: 1461858Hom.: 1 Cov.: 30 AF XY: 0.000213 AC XY: 155AN XY: 727220
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GnomAD4 genome AF: 0.000893 AC: 136AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74484
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
DHX38-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 22, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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DANN
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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