ClinVar Miner

Submissions for variant NM_001033855.3(DCLRE1C):c.959C>G (p.Ser320Cys)

gnomAD frequency: 0.01123  dbSNP: rs41298896
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen RCV001083680 SCV004102780 benign Severe combined immunodeficiency due to DCLRE1C deficiency 2023-11-14 reviewed by expert panel curation The NM_001033855.3:c.959C>G variant in DCLRE1C is a missense variant predicted to cause substitution of serine by cysteine at amino acid 320 (p.Ser320Cys). This variant has an allele frequency of 0.03553 in the African / African American population in gnomAD, which is above the threshold for BA1 set by the ClinGen SCID VCEP for DCLRE1C (>0.00346). In addition, 16 adult homozygous individuals with this variant are present in gnomAD v2.1.1 (in African/African American population)(BS2_Supporting). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive SCID based on the ACMG criteria applied: BA1 and BS2_Supporting as specified by the ClinGen SCID VCEP (VCEP specifications version 1).
GeneDx RCV000124664 SCV000168097 benign not provided 2018-12-17 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 26915675)
Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre RCV000124664 SCV000221370 likely pathogenic not provided criteria provided, single submitter research
Illumina Laboratory Services, Illumina RCV000348357 SCV000361552 benign Histiocytic medullary reticulosis 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.
Invitae RCV001083680 SCV000645230 benign Severe combined immunodeficiency due to DCLRE1C deficiency 2024-01-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000124664 SCV001473590 benign not provided 2020-08-27 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000124664 SCV004126478 benign not provided 2023-02-01 criteria provided, single submitter clinical testing DCLRE1C: BS1, BS2
Natera, Inc. RCV001831916 SCV002082295 likely benign Athabaskan severe combined immunodeficiency 2019-11-12 no assertion criteria provided clinical testing

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