11-126306583-C-CTGGGGA
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2
The NM_014026.6(DCPS):c.225_230dup(p.Asp76_Gly77dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0177 in 1,608,582 control chromosomes in the GnomAD database, including 384 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 20 hom., cov: 31)
Exomes 𝑓: 0.018 ( 364 hom. )
Consequence
DCPS
NM_014026.6 inframe_insertion
NM_014026.6 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.419
Genes affected
DCPS (HGNC:29812): (decapping enzyme, scavenger) This gene encodes a member of the histidine triad family of pyrophosphatases that removes short mRNA fragments containing the 5′ mRNA cap structure, which appear in the 3′ → 5′ mRNA decay pathway, following deadenylation and exosome-mediated turnover. This enzyme hydrolyzes the triphosphate linkage of the cap structure (7-methylguanosine nucleoside triphosphate) to yield 7-methylguanosine monophosphate and nucleoside diphosphate. It protects the cell from the potentially toxic accumulation of these short, capped mRNA fragments, and regulates the activity of other cap-binding proteins, which are inhibited by their accumulation. It also acts as a transcript-specific modulator of pre-mRNA splicing and microRNA turnover. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_014026.6.
BP6
?
Variant 11-126306583-C-CTGGGGA is Benign according to our data. Variant chr11-126306583-C-CTGGGGA is described in ClinVar as [Benign]. Clinvar id is 3068672.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0123 (1875/152182) while in subpopulation SAS AF= 0.0357 (172/4814). AF 95% confidence interval is 0.0314. There are 20 homozygotes in gnomad4. There are 902 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 20 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCPS | NM_014026.6 | c.225_230dup | p.Asp76_Gly77dup | inframe_insertion | 2/6 | ENST00000263579.5 | |
DCPS | NM_001350236.2 | c.246_251dup | p.Asp83_Gly84dup | inframe_insertion | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCPS | ENST00000263579.5 | c.225_230dup | p.Asp76_Gly77dup | inframe_insertion | 2/6 | 1 | NM_014026.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0123 AC: 1876AN: 152064Hom.: 20 Cov.: 31
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GnomAD3 exomes AF: 0.0173 AC: 4283AN: 247900Hom.: 60 AF XY: 0.0190 AC XY: 2552AN XY: 134122
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GnomAD4 exome AF: 0.0183 AC: 26676AN: 1456400Hom.: 364 Cov.: 30 AF XY: 0.0192 AC XY: 13923AN XY: 723458
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Al-Raqad syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | May 04, 2023 | South Asian population allele frequency is 3.731% (rs201095573,1185/30256 alleles, 32 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.5.1, this variant is classified as BENIGN. Following criteria are met: BA1 - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at