Submissions for variant NM_000376.3(VDR):c.2T>C (p.Met1Thr)

gnomAD frequency: 0.66221  dbSNP: rs2228570

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000988816	SCV000378929	benign	Vitamin D-dependent rickets type II with alopecia	2018-03-06	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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000601968	SCV000711761	benign	not specified	2016-02-17	criteria provided, single submitter	clinical testing	This is a RefSeq error, the reference base (c.152T) is the minor allele. This a llele (T) has been identified in 48% (5540/11550) of Latino chromosomes by the E xome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs22285 70) and thus meets the criteria to be classified as benign.
Mendelics	RCV000988816	SCV001138701	benign	Vitamin D-dependent rickets type II with alopecia	2019-05-28	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV001512350	SCV001719750	benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing
GeneDx	RCV001512350	SCV001950551	benign	not provided	2018-08-16	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 16019132, 12807755, 20473893, 18752562, 19131500, 15899948, 21283672, 21814771, 18763633, 9169350, 23855914, 30092343, 27939971, 21820934, 29506625, 22181683, 23286944, 24078452, 24702903, 24771013, 27683185)
Genome-Nilou Lab	RCV000988816	SCV002514469	benign	Vitamin D-dependent rickets type II with alopecia	2021-12-05	criteria provided, single submitter	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000601968	SCV001741570	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000601968	SCV001958323	benign	not specified		no assertion criteria provided	clinical testing
Laboratory of Cyto-molecular Genetics, Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi	RCV000988816	SCV002102810	likely pathogenic	Vitamin D-dependent rickets type II with alopecia	2022-03-07	flagged submission	clinical testing
Genetics Laboratory, Lanzhou University	RCV003992273	SCV004812010	benign	Periodontitis	2023-04-20	no assertion criteria provided	case-control