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Table 3 Top results of the genome-wide burden analysis for rare variants increasing the risk of life-threatening COVID-19 under a recessive model

From: Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Chr

Gene

Variant set

Type of variant

CADD > MSCa

GnomAD AF threshold

No. carriers of at least one rare homo-/hemizygous variant

Joint analysis

Trans-ethnic meta-analysis

Trans-pipeline meta-analysis

Cases (n = 3269)

Controls (n = 1373)

OR[95%CI]

P value

GW analysis

 

 X

TLR7

7

MISSLOF

FALSE

0.01

51

2

8.41 [1.9–35.5]

8.95 × 10−5

7.04 × 10−4

2.66 × 10−4

 14

AHNAK2

5

MISSLOF

TRUE

0.001

37

2

4.45 [1.1–17.7]

0.01

2.15 × 10−3

8.84 × 10−3

Refined analysis on TLR7

 

 X

TLR7

 

bLOF

-

0.01

20

0

27.68[1.5–528.7]

1.1 × 10−4

6.6 × 10−3

2.7 × 10−4

  1. Only genes with P values ≤ 0.01 in the joint analysis and P values < 0.05 in trans-ethnic and trans-pipeline meta-analyses are displayed
  2. AF allele frequency
  3. aCombined Annotation Dependent Depletion (CADD) score [42] greater than the Mutation Significance Cut-off (MSC) for the corresponding gene. The MSC is defined for a given gene as the lower limit of the confidence interval (95%) of the CADD score of all its known pathogenic mutations [43]
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Genome Medicine

ISSN: 1756-994X

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