1-193122189-A-AG
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_024529.5(CDC73):c.-4dupG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00858 in 1,608,664 control chromosomes in the GnomAD database, including 67 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0062 ( 8 hom., cov: 32)
Exomes 𝑓: 0.0088 ( 59 hom. )
Consequence
CDC73
NM_024529.5 5_prime_UTR
NM_024529.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.51
Genes affected
CDC73 (HGNC:16783): (cell division cycle 73) This gene encodes a tumor suppressor that is involved in transcriptional and post-transcriptional control pathways. The protein is a component of the the PAF protein complex, which associates with the RNA polymerase II subunit POLR2A and with a histone methyltransferase complex. This protein appears to facilitate the association of 3' mRNA processing factors with actively-transcribed chromatin. Mutations in this gene have been linked to hyperparathyroidism-jaw tumor syndrome, familial isolated hyperparathyroidism, and parathyroid carcinoma. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
Variant 1-193122189-A-AG is Benign according to our data. Variant chr1-193122189-A-AG is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 286328.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=3, Likely_benign=2, Benign=6}.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0062 (942/151816) while in subpopulation NFE AF= 0.00939 (637/67872). AF 95% confidence interval is 0.00878. There are 8 homozygotes in gnomad4. There are 462 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 942 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00620 AC: 940AN: 151700Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00729 AC: 1785AN: 244892Hom.: 14 AF XY: 0.00745 AC XY: 993AN XY: 133210
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GnomAD4 exome AF: 0.00883 AC: 12861AN: 1456848Hom.: 59 Cov.: 32 AF XY: 0.00883 AC XY: 6400AN XY: 724476
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GnomAD4 genome AF: 0.00620 AC: 942AN: 151816Hom.: 8 Cov.: 32 AF XY: 0.00622 AC XY: 462AN XY: 74226
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:3Benign:9
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 22, 2017 | This variant is associated with the following publications: (PMID: 28774260) - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | CDC73: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 28, 2016 | Variant summary: c.-4dupG is located in the 5UTR region. Mutation taster predicts deleterious outcome. 4/5 in silico tools in Alamut predict no significant change on splicing pattern, however, these predictions should be taken with caution as Alamut tools are not meant to analyze UTR regions. The variant is present in the control population dataset of ExAC at frequency of 0.94%, predominantly in individuals of European descent (1.2%), including several homozygous occurrences. The observed frequency greatly exceeds the maximum expected allele frequency for a pathogenic variant of 0.0004%, suggesting that it is a benign polymorphism. The variant of interest has not, to our knowledge, been reported in affected individuals but cited as "Benign" by a clinical laboratory. Taking together, based on the prevalence of this variant in general population the variant was classified as Benign. - |
Likely benign, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
Parathyroid carcinoma Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 25, 2016 | - - |
Isolated Hyperparathyroidism Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Hyperparathyroidism 2 with jaw tumors Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
CDC73-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 30, 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). - |
Hereditary cancer-predisposing syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 21, 2018 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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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