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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

From: ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden

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