chr5-177511790-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_016222.4(DDX41):c.*1G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,614,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000024 ( 0 hom. )
Consequence
DDX41
NM_016222.4 3_prime_UTR
NM_016222.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.965
Genes affected
DDX41 (HGNC:18674): (DEAD-box helicase 41) 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 the DEAD box protein 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 box protein family and interacts with several spliceosomal proteins. In addition, the encoded protein may recognize the bacterial second messengers cyclic di-GMP and cyclic di-AMP, resulting in the induction of genes involved in the innate immune response. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
?
Variant 5-177511790-C-T is Benign according to our data. Variant chr5-177511790-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3054698.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX41 | NM_016222.4 | c.*1G>A | 3_prime_UTR_variant | 17/17 | ENST00000330503.12 | ||
DDX41 | NM_001321732.2 | c.*1G>A | 3_prime_UTR_variant | 16/16 | |||
DDX41 | NM_001321830.2 | c.*1G>A | 3_prime_UTR_variant | 17/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX41 | ENST00000330503.12 | c.*1G>A | 3_prime_UTR_variant | 17/17 | 1 | NM_016222.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152186Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000841 AC: 21AN: 249762Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135140
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GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461760Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 16AN XY: 727164
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GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74476
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
DDX41-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 30, 2023 | 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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Name
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BayesDel_noAF
Benign
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Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at