Table 1 Subset of ClinVar variants seen in a pathogenic genotype in 1KGP. See Additional file 6: Table S4 for the full list of ClinVar variants. NC indicates no assertion criteria were provided by the submitter
Chr | Position in GRCh38 | Ref | Alt | Gene, transcript ID | cDNA, protein | No. of hom or hemi in 1KGP | No. of comp het in 1KGP | 1KGP sample ID(s) | First pathogenic submission: submitter, date, interpretation, evidence | Consensus interpretation as of December 2020 | Submitted interpretations |
|---|---|---|---|---|---|---|---|---|---|---|---|
9 | 130,458,549 | G | T | ASS1, NM_054012.4 | c.323G > T R108L | 1 | 1 | NA19030 NA19395 | OMIM, April 2014, Pathogenic NC, heterozygous variant in affected individual | Conflicting Interpretations of Pathogenicity | 1 Pathogenic NC 1 VUS 4 Likely Benign 1 Benign 1 Benign NC |
12 | 109,561,798 | C | T | MMAB, NM_052845.4 | c.403G > A p.A135T | 1 | 0 | HG03169 | GeneReviews, February 2016, Pathogenic NC, seen in affected individuals | Conflicting Interpretations of Pathogenicity | 1 Pathogenic NC 1 VUS 1 Benign 1 Benign NC |
12 | 120,739,317 | A | G | ACADS, NM_000017.4 | c.1108A > G p.M370V | 1 | 0 | NA20878 | GeneDx, August 2015, Pathogenic, clinical testing | Conflicting Interpretations of Pathogenicity | 2 VUS 1 Likely Benign |
X | 38,367,361 | G | A | OTC, NM_000531.6 | c.148G > A p.G50R | 1 | 0 | NA21124 | GenMed Metabolism Lab, April 2014, Pathogenic NC, identified in late-onset individual | Pathogenic, 0 stars | 2 Pathogenic NC |