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Table 1 Most common variants in the curated patient dataset

From: Predicting disease severity in metachromatic leukodystrophy using protein activity and a patient phenotype matrix

Reference SNP ID

Genomic coordinate GRCh37

HGVSc

HGVSp

Patient count, n

ClinVar pathogenicity

Patient-based severity

CDS activity-based severity

CDS percentage of wild-type activity, %

Overall gnomAD frequency

gnomAD population maximum frequency

gnomAD population

rs80338815

chr22:51065593:C > T

c.465 + 1G > A

NA

186

Pathogenic

Severe

NA

NA

6.36E − 04

1.21E − 03

NFE

rs28940893

chr22:51063820:G > A

c.1283C > T

p.P428L

117

Pathogenic

Moderate

Severe

0.037

4.08E − 04

9.47E − 04

Other

rs74315457

chr22:51065404:A > C

c.542 T > G

p.I181S

25

Pathogenic

Mild

Mild

4.32

2.26E − 04

4.06E − 04

Finnish

rs551472773

chr22:51064624:G > A

c.937C > T

p.R313X

18

Pathogenic

Severe

NA

NA

1.26E − 05

2.79E − 05

NFE

rs74315458

chr22:51065802:C > T

c.257G > A

p.R86Q

15

Pathogenic

Moderate

Moderate

2.13

8.09E − 05

2.74E − 04

Finnish

rs199476352

chr22:51065803:G > A

c.256C > T

p.R86W

14

Conflicting interpretations of pathogenicity

Moderate

Mild

7.86

NA

NA

NA

rs74315455

chr22:51065757:C > A

c.302G > T

p.G101V

13

Pathogenic

Severe

Severe

0.069

NA

NA

NA

rs74315459

chr22:51064630:C > T

c.931G > A

p.G311S

12

Conflicting interpretations of pathogenicity

Severe

Severe

0.28

2.92E − 05

9.94E − 05

South Asian

rs74315480

chr22:51064043:G > A

c.1174C > T

p.R392W

12

Conflicting interpretations of pathogenicity

Severe

Severe

0.20

1.63E − 05

6.50E − 05

South Asian

rs74315472

chr22:51065046:G > A

c.827C > T

p.T276M

12

Pathogenic / likely pathogenic

Severe

Severe

0.098

4.07E − 06

1.82E − 04

Other

rs743616

chr22:51064039:G > C

c.1178C > G

p.T393S

11

Benign

Benign

Benign

14.69

4.82E − 01

5.93E − 01

Finnish

rs199476360

chr22:51064636:C > T

c.925G > A

p.E309K

11

Pathogenic

Severe

Severe

1.36

4.14E − 06

5.87E − 05

East Asian

rs74315481

chr22:51063872:TGGTATCAC > -

c.1223_1231delGTGATACCA

p.S408_T410del

10

Pathogenic / likely pathogenic

Severe

Severe

0.23

8.53E − 06

9.50E − 06

NFE

  1. CDS Coding sequence, gnomAD Genome Aggregation Database, HGVSc Human Genome Variation Society coding variant, HGVSp Human Genome Variation Society protein variant, NA Not applicable, NFE Non-Finnish European, SNP Single-nucleotide polymorphism