ClinVar Miner

Submissions for variant NM_000528.4(MAN2B1):c.2006C>T (p.Pro669Leu)

gnomAD frequency: 0.00451  dbSNP: rs75029862
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia RCV000203001 SCV000257701 benign not specified 2015-02-05 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000224345 SCV000281422 benign not provided 2014-12-09 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000203001 SCV000331144 benign not specified 2016-04-18 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000260388 SCV000410786 benign Deficiency of alpha-mannosidase 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV000260388 SCV000752986 benign Deficiency of alpha-mannosidase 2024-02-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000203001 SCV000919598 benign not specified 2017-11-08 criteria provided, single submitter clinical testing Variant summary: The MAN2B1 c.2006C>T (p.Pro669Leu) variant involves the alteration of a conserved nucleotide and 3/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 2336/277222 (34 homozygotes) control chromosomes (gnomAD) at a frequency of 0.0084265, which is approximately 5 times the estimated maximal expected allele frequency of a pathogenic MAN2B1 variant (0.0015811), suggesting this variant is likely a benign polymorphism. Functional study showed variant with comparable level of activity as wild type (Stensland_015). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as "likely benign/benign." Taken together, this variant is classified as benign.
GeneDx RCV000224345 SCV001765411 likely benign not provided 2022-06-08 criteria provided, single submitter clinical testing See Variant Classification Assertion Criteria.
Fulgent Genetics, Fulgent Genetics RCV000260388 SCV002804298 benign Deficiency of alpha-mannosidase 2021-07-07 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000224345 SCV000801168 benign not provided 2015-12-16 no assertion criteria provided clinical testing

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