ClinVar Miner

Submissions for variant NM_015559.3(SETBP1):c.2117A>G (p.Glu706Gly)

gnomAD frequency: 0.00002  dbSNP: rs530739140
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001354400 SCV002158052 benign not provided 2023-12-04 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV001354400 SCV003819372 uncertain significance not provided 2019-10-08 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV001354400 SCV005193313 uncertain significance not provided criteria provided, single submitter not provided
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001354400 SCV001549009 uncertain significance not provided no assertion criteria provided clinical testing The SETBP1 p.Glu706Gly variant was not identified in the literature nor was it identified in ClinVar, Cosmic, and LOVD 3.0 databases, however the variant was identified in dbSNP (ID: rs530739140). The variant was identified in control databases in 6 of 251000 chromosomes at a frequency of 0.000024 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the European (non-Finnish) population in 6 of 113382 chromosomes (freq: 0.000053), while the variant was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish), Other or South Asian populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, and GeneSplicer) do not predict a difference in splicing. The p.Glu706 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, and MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. 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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