Submissions for variant NM_182760.4(SUMF1):c.1116T>C (p.Thr372=)

gnomAD frequency: 0.66322  dbSNP: rs2633852

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000082714	SCV000114758	benign	not specified	2013-04-26	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000082714	SCV000316758	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000325033	SCV000444461	benign	Multiple sulfatase deficiency	2018-01-12	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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000082714	SCV000918295	benign	not specified	2017-12-29	criteria provided, single submitter	clinical testing	Variant summary: The SUMF1 c.1116T>C (p.Thr372Thr) variant involves the alteration of a non-conserved nucleotide causes a synonymous change and 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may alter ESE binding. This variant was found in 176669/274930 control chromosomes (58685 homozygotes)(gnomAD) at a frequency of 0.6425963, which is approximately 575 times the estimated maximal expected allele frequency of a pathogenic SUMF1 variant (0.001118). The observed frequency the C allele, 0.64, indicates the variant of interest to be the major allele (allele more commonly observed in the general population). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Invitae	RCV000325033	SCV001728601	benign	Multiple sulfatase deficiency	2024-02-01	criteria provided, single submitter	clinical testing
Pars Genome Lab	RCV000325033	SCV001738670	benign	Multiple sulfatase deficiency	2021-06-15	criteria provided, single submitter	clinical testing
GeneDx	RCV000675756	SCV001867365	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000325033	SCV002062298	benign	Multiple sulfatase deficiency	2021-07-15	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000675756	SCV000801476	benign	not provided	2015-10-22	no assertion criteria provided	clinical testing
Natera, Inc.	RCV000325033	SCV001460167	benign	Multiple sulfatase deficiency	2020-09-16	no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000082714	SCV001741193	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000082714	SCV001960026	benign	not specified		no assertion criteria provided	clinical testing