Table 1 Categories of small variants in non-coding regions previously implicated in penetrant Mendelian disease

Promoter

Altering transcription factor binding

GATA1:−113A>G

Hereditary persistence of foetal haemoglobin

1

Upstream gene variant / regulatory region / TF binding site

TF binding site disruption prediction tools e.g. motifbreakR / SEMpl / QBiC-Pred

Promoter

Altering transcription

CHM c.-98C>A, c.-98C>T

Choroideremia

2

Promoter/5′UTR

Altering methylation patterns

BRCA1:c.-107A>T

Breast and ovarian cancer

3

Upstream gene variant / 5 prime UTR variant

5′UTR

Creating upstream start site (uAUG)

NF1:c.-272G>A

Neurofibromatosis type 1

1013130

4

5 prime UTR variant

e.g. UTRannotator

5′UTR

Perturbing upstream open reading frames

NF2:−66-65insT

Neurofibromatosis type 2

5

e.g. UTRannotator

5′UTR

Disrupting internal ribosome entry sites (IRES)

GJB1:c.-103C>T

Charcot-Marie-Tooth disease

217166

6

e.g. IRESpy / IRESfinder / IRESite

5′UTR

Disrupting splicing

SHOX:c.-19G>A

SHOX haploinsufficiency

933226

7

Splicing prediction tools e.g. SpliceAI

5′UTR

Altering Kozak consensus of start site

GATA4:c.-6G>C

Atrial septal defect

8

e.g. utR.annotation

5′UTR

N-terminal transcript elongation

MEF2C:c.−8C>T

Developmental disorder

9

e.g. UTRannotator

Intron

Disrupting canonical splice sites

MYBPC3:c.3490+1G>A

Hypertrophic cardiomyopathy

42715

10

Splice donor variant / splice acceptor variant / splice region variant / splice_donor_5th_base_variant / splice_polypyrimidine_tract_variant

Splicing prediction tools e.g. SpliceAI

Intron

Disrupting splicing branch point

HNF4A:c.264-21A>G

Maturity-onset diabetes of the young

11

Intron variant

Splicing prediction tools e.g. SpliceAI

Intron

Pseudo-exon activation

DMD: c.7310-19A>G

Muscular dystrophy

12

Splicing prediction tools e.g. SpliceAI

Intron

Poison-exon inclusion

SCN1A:c.4002+2165C>T

Dravet Syndrome

13

Splicing prediction tools e.g. SpliceAI

Intron

Branchpoint mutation

BBS1:c.592-21A>T

Retinitis pigmentosa

14

Splicing prediction tools e.g. SpliceAI

Intron

Indels & spacing of splicing motifs

DOK7:c.54+8_54+17del

15

Splicing prediction tools e.g. SpliceAI

Intron

Cryptic exon

VHL: c.3401770T.C

Erythrocytosis

16

3′UTR

Disrupting polyA signal motif

NAA10:c.^a43A>G

Microphthalmia

617463

17

3 prime UTR variant

PolyA signal motif prediction tools e.g. Omni-PolyA

3′UTR

Disrupting miRNA interactions

REEP1

Hereditary spastic paraplegia

18

miRNA binding site prediction e.g. miRTarBase

3′UTR

Disrupting splicing

LHFPL5:c.^a16+1G>A

Hearing impairment

19

Splicing prediction tools e.g. SpliceAI

CRE

Altering transcription factor binding

chr7:155754267:C>T; NCBI build 36.3

Holoprosencephaly

20

Upstream gene variant / downstream gene variant / regulatory region variant / TF binding site variant / intergenic variant / TFBS ablation / TFBS amplification / regulatory region ablation / regulatory region amplification

TF binding site disruption prediction tools e.g. motifbreakR / SEMpl / QBiC-Pred

CRE

Abolishing enhancer activity

PTF1A - 6 variants

Isolated pancreatic agenesis

21

CRE

Disrupting enhancer activity

SOX9 - deletion (chr17:67,628,756–67,634,155)

Pierre Robin sequence

22

Intergenic

Creating new regulatory element

chr16:209,709 T>C

α-thalassaemia

23

Intergenic variant / upstream gene variant / downstream gene variant

miRNA

Disrupting seed region

miR-204:n.37C>T

Retinal dystrophy

24

non-coding transcript exon variant / non-coding transcript variant / mature_miRNA_variant

snRNA

Altering structure

RNU12

Cerebellar ataxia

25

Non-coding transcript exon variant / non-coding transcript variant

snRNA

Abnormal splicing, accumulation of minor intron retained transcripts

RNU4ATAC

Roifman Syndrome

26

Splicing prediction tools e.g. SpliceAI

snRNA

Affecting expression, processing and protein binding

SNORD118

Cerebral microangiopathy leukoencephalopathy

27

TAD boundary

Disrupting chromatin looping leading to enhancer loss or adoption

WNT6/IHH/EPHA4/PAX3 locus

Limb phenotypes

28

Intergenic variant