Table 5 Five non-coding variants in the MYOC region remain following initial filtering of the 160 non-coding variants with FATHMM ≥0.5.

From: Comprehensive sequencing of the myocilin gene in a selected cohort of severe primary open-angle glaucoma patients

No.

Feature

Chrom

POS

Ref

Alt

dbSNP144

1000 G EUR

Sample count

Study AF

gerp++ gt2

FATHMM

CADD Phred

myocDB

Repeat

PhastCons

Regulatory build

1

INTERGENIC_US

chr1

171655462

C

T

—

—

1

0.00140

3.22

0.593

11.19

—

0

0.008

CTCF Binding Site

2

INTRON1

chr1

171,646,066

C

T

rs12035960

0.10440

55

0.08200

3.57

0.860

12.78

—

0

0.504

Promoter Flanking Region

3

INTRON1

chr1

171,644,671

G

A

rs75953590

0.01990

16

0.02200

—

0.551

15.38

—

0

0.244

—

4

INTRON1

chr1

171,643,942

G

C

rs144750384

0.00800

1

0.00150

—

0.623

10.31

—

1

0.061

Open chromatin

5

INTRON2

chr1

171,637,310

A

G

rs79263003

0.01090

10

0.01400

—

0.570

4.669

—

0

0.280

—

  1. Feature, genetic feature within MYOC; Chrom, chromosome; POS, location of 5′ base of variant in hg38; Ref, reference allele; Alt, alternate allele; dbSNP144, rsID if the variant is known; 1000 G EUR, allele frequency from 1000 Genomes Project (European ethnic sub-group); Sample count, number of patients with the variant in the n = 358 POAG cohort; Study AF, allele frequency of the variant within the n = 358 POAG cohort; gerp++, Genomic Evolutionary Rate Profiling; FATHMM, Functional Analysis through Hidden Markov Models; CADD Phred, Combined Annotation Dependent Depletion on a Phred scale; myocDB, known MYOC variants database24; Repeat, repetitive region as defined by RepeatMasker; PhastCons, conservation scoring and identification of conserved elements; Regulatory build, Ensembl Regulatory Build containing regions that are likely to be involved in gene regulation.
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