ClinVar Miner

Submissions for variant NM_005228.5(EGFR):c.1509C>T (p.Gly503=)

gnomAD frequency: 0.00859  dbSNP: rs17336800
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000860980 SCV001001172 benign EGFR-related lung cancer 2024-02-01 criteria provided, single submitter clinical testing
GeneDx RCV001544693 SCV001763868 likely benign not provided 2020-09-15 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV001356543 SCV002069901 benign not specified 2021-07-26 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001544693 SCV002545514 benign not provided 2024-08-01 criteria provided, single submitter clinical testing EGFR: BP4, BP7, BS1, BS2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001544693 SCV004563086 benign not provided 2023-10-16 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV001544693 SCV005227365 likely benign not provided criteria provided, single submitter not provided
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001356543 SCV001551744 benign not specified no assertion criteria provided clinical testing The EGFR p.Gly503Gly variant was identified in the literature in a Korean cohort of 27 lung cancer cases (frequency: 0.41) and 27 controls (frequency: 0.41) (Choi_2007_PMID:12956637). The variant was also identified in a case report of an individual with suspected plasma cell neoplasm (Peterson_2019_PMID:31320253). The variant was identified in dbSNP (ID: rs17336800), ClinVar (classified as benign by Invitae) and LOVD 3.0, but was not identified in Cosmic. The variant was identified in control databases in 2092 of 267912 chromosomes (14 homozygous) at a frequency of 0.007809 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (Finnish) in 348 of 24930 chromosomes (freq: 0.01396), European (non-Finnish) in 1370 of 117988 chromosomes (freq: 0.01161), Other in 75 of 6696 chromosomes (freq: 0.0112), Latino in 163 of 35096 chromosomes (freq: 0.004644), Ashkenazi Jewish in 24 of 9852 chromosomes (freq: 0.002436), South Asian in 67 of 30502 chromosomes (freq: 0.002197) and African in 45 of 23606 chromosomes (freq: 0.001906), but was not observed in the East Asian population. The p.Gly503Gly variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. However, three of four in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing and the creation of a new 5' splice site. However, this has not been confirmed by RNA analysis and is not predictive enough to assume pathogenicity. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.

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