Submissions for variant NM_000141.5(FGFR2):c.23T>G (p.Ile8Ser) (rs147307031)

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics	RCV000121062	SCV000332753	benign	not specified	2015-07-01	criteria provided, single submitter	clinical testing
Invitae	RCV001078866	SCV000777352	benign	FGFR2 related craniosynostosis	2019-12-31	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000756160	SCV000883886	likely benign	not provided	2018-03-25	criteria provided, single submitter	clinical testing	The c.23T>G; p.Ile8Ser variant (rs147307031) has been reported in a patient with craniosynostosis; however, this patient also harbored another pathogenic variant, and the authors classified the p.Ile8Ser variant as “not pathogenic” (Goos 2015). This variant was also detected in a cohort of healthy individuals (Bodian 2014), is listed in the genome Aggregation Database (gnomAD) with an African population frequency of 0.3% (identified on 63 out of 24,026 chromosomes, including one homozygote) and is classified as benign in ClinVar (variant ID: 134388). The isoleucine at position 8 is weakly conserved, considering 12 species, and computational analyses of the effects of the p.Ile8Ser variant on protein structure and function make conflicting predictions (SIFT: damaging, PolyPhen-2: benign ). Based on the available information, the p.Ile8Ser variant is likely to be benign.
Illumina Clinical Services Laboratory,Illumina	RCV001103882	SCV001260695	uncertain significance	Isolated coronal synostosis	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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Clinical Services Laboratory,Illumina	RCV001103883	SCV001260696	benign	Saethre-Chotzen syndrome	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.
Illumina Clinical Services Laboratory,Illumina	RCV001103884	SCV001260697	benign	Craniosynostosis	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.
Illumina Clinical Services Laboratory,Illumina	RCV001107510	SCV001264661	benign	Beare-Stevenson cutis gyrata syndrome	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.
Illumina Clinical Services Laboratory,Illumina	RCV001107511	SCV001264662	benign	Crouzon syndrome	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.
ITMI	RCV000121062	SCV000085230	not provided	not specified	2013-09-19	no assertion provided	reference population