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