ClinVar Miner

Submissions for variant NM_032119.4(ADGRV1):c.9447+6G>A (rs201481219)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000150766 SCV000198252 likely benign not specified 2015-06-19 criteria provided, single submitter clinical testing c.9447+6G>A in intron 6 of GPR98: This variant is not expected to have clinical significance because it has been identified in 0.3% (32/11530) of Latino chromos omes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs201481219).
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia RCV000150766 SCV000297336 likely benign not specified 2015-10-31 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000724883 SCV000332145 uncertain significance not provided 2015-06-23 criteria provided, single submitter clinical testing
Invitae RCV000724883 SCV001034043 likely benign not provided 2020-11-21 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000724883 SCV001154443 uncertain significance not provided 2018-10-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001157221 SCV001318772 uncertain significance Usher syndrome, type 2C 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.
Athena Diagnostics Inc RCV000724883 SCV001476092 likely benign not provided 2020-02-11 criteria provided, single submitter clinical testing
GeneDx RCV000724883 SCV001872540 benign not provided 2020-06-25 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000724883 SCV001553697 uncertain significance not provided no assertion criteria provided clinical testing The ADGRV1 c.9447+6G>A variant was not identified in the literature but was identified in dbSNP (ID: rs201481219) and ClinVar (classified as a VUS by EGL Genetics and as likely benign by Laboratory for Molecular Medicine and Division of Genomic Diagnostics at The Children's Hospital of Philadelphia). The variant was also identified in control databases in 246 of 277482 chromosomes at a frequency of 0.000887 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Ashkenazi Jewish in 32 of 10164 chromosomes (freq: 0.003148), Latino in 78 of 34728 chromosomes (freq: 0.002246), Other in 7 of 7030 chromosomes (freq: 0.000996), African in 19 of 24152 chromosomes (freq: 0.000787), European (non-Finnish) in 96 of 127122 chromosomes (freq: 0.000755), South Asian in 13 of 30042 chromosomes (freq: 0.000433) and European (Finnish) in 1 of 24812 chromosomes (freq: 0.00004), but was not observed in the East Asian population. The c.9447+6G>A variant is located in the 5' splice region but does not affect the invariant +1 and +2 positions. However, positions +3 to +6 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In addition, 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 splicing prediction has not been confirmed by RNA analysis. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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