3-138161853-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016216.4(DBR1):c.*36T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 1,552,550 control chromosomes in the GnomAD database, including 354,892 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.62 ( 30256 hom., cov: 33)
Exomes 𝑓: 0.68 ( 324636 hom. )
Consequence
DBR1
NM_016216.4 3_prime_UTR
NM_016216.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0250
Genes affected
DBR1 (HGNC:15594): (debranching RNA lariats 1) The protein encoded by this gene is an RNA lariat debranching enzyme that hydrolyzes 2'-5' prime branched phosphodiester bonds. The encoded protein specifically targets the bonds at the branch point of excised lariat intron RNA, converting them to linear molecules that are then degraded. This protein may also be involved in retroviral replication. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 3-138161853-A-G is Benign according to our data. Variant chr3-138161853-A-G is described in ClinVar as [Benign]. Clinvar id is 2687947.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DBR1 | NM_016216.4 | c.*36T>C | 3_prime_UTR_variant | 8/8 | ENST00000260803.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DBR1 | ENST00000260803.9 | c.*36T>C | 3_prime_UTR_variant | 8/8 | 1 | NM_016216.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.624 AC: 94848AN: 151962Hom.: 30247 Cov.: 33
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GnomAD3 exomes AF: 0.648 AC: 156163AN: 241066Hom.: 51039 AF XY: 0.652 AC XY: 84663AN XY: 129842
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GnomAD4 exome AF: 0.679 AC: 950412AN: 1400470Hom.: 324636 Cov.: 23 AF XY: 0.677 AC XY: 472681AN XY: 697796
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GnomAD4 genome AF: 0.624 AC: 94894AN: 152080Hom.: 30256 Cov.: 33 AF XY: 0.624 AC XY: 46416AN XY: 74360
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 89% of patients studied by a panel of primary immunodeficiencies. Number of patients: 85. Only high quality variants are reported. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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