Variant Numbering and Syntax Rules:
Correlagen's conventions for numbering and naming sequence variants follow the recommendations
by the Human Genome Variation Society and are described in detail in the tables and figures below.
Generic rules are given as well as specific examples.
Generic Rules
- Variant Numbering
- Variant Syntax
- Substitution
- Deletion
- Deletion of Single Nucleotide
- Deletion of >1 but <=20 Nucleotides
- Deletion of >20 Nucleotides
- Deletion/Insertion
- Insertion
- Duplication
| Variant Numbering |
| Exon 1 |
Intron 1 |
Exon 2 |
Intron 2 |
Exon 3 |
| 5'UTR |
|
5'UTR |
Met |
Glu |
|
Val |
stop |
3'UTR |
| G |
A |
G |
G |
T |
A |
G |
G |
T |
A |
T |
G |
G |
A |
G |
G |
T |
A |
G |
G |
T |
A |
T |
G |
A |
G |
A |
| -5 |
-4 |
-3 |
-3+1 |
-3+2 |
-2-2 |
-2-1 |
-2 |
-1 |
1 |
2 |
3 |
4 |
5 |
6 |
6+1 |
6+2 |
7-2 |
7-1 |
7 |
8 |
9 |
10 |
11 |
12 |
13 |
14 |
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| Syntax for Substitution in Exon |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
6 |
| A |
T |
G |
G |
A |
A |
variant sequence
correct notation: c.1A>G |
G |
T |
G |
G |
A |
A |
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| Syntax for Substitution in Intron |
| reference sequence |
5 |
6 |
6+1 |
6+2 |
6+3 |
6+4 |
| A |
G |
G |
T |
A |
A |
variant sequence
correct notation: c.6+2T>G |
A |
G |
G |
G |
A |
A |
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| Syntax for Deletion of Single Nucleotide in Exon |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
| A |
C |
T |
T |
T |
G |
T |
G |
C |
C |
variant sequence
correct notation: c.5delT |
A |
C |
T |
T |
|
G |
T |
G |
C |
C |
| Note: If different deletions can lead to the same variant sequence, the deletion is entered as having occurred at the most 3' position possible. |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
| A |
C |
T |
T |
T |
G |
T |
G |
C |
C |
variant sequence
incorrect notation: c.4delT |
A |
C |
T |
|
T |
G |
T |
G |
C |
C |
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| Syntax for Deletion of Single Nucleotide in Intron |
| reference sequence |
6 |
6+1 |
6+2 |
6+3 |
6+4 |
6+5 |
| G |
G |
T |
A |
A |
G |
variant sequence
correct notation: c.6+4delA |
C |
T |
T |
A |
|
G |
| Note: If different deletions can lead to the same variant sequence, the deletion is entered as having occurred at the most 3' position possible. |
| reference sequence |
6 |
6+1 |
6+2 |
6+3 |
6+4 |
6+5 |
| G |
G |
T |
A |
A |
G |
variant sequence
incorrect notation: c.6+3delA |
C |
T |
T |
|
A |
G |
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| Syntax for Deletion of >1 but <=20 Nucleotides in Exon |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
| A |
C |
T |
T |
T |
G |
T |
G |
C |
C |
variant sequence
correct notation: c.5_7delTGT |
A |
C |
T |
T |
|
|
|
G |
C |
C |
| Note: If different deletions can lead to the same variant sequence, the deletion is entered as having occurred at the most 3' position possible. |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
| A |
C |
T |
T |
T |
G |
T |
G |
C |
C |
variant sequence
incorrect notation: c.4_6delTTG |
A |
C |
T |
|
|
|
T |
G |
C |
C |
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| Syntax for Deletion of >1 but <=20 Nucleotides in Intron |
| reference sequence |
6+5 |
6+6 |
6+7 |
6+8 |
6+9 |
6+10 |
| G |
T |
A |
A |
A |
G |
variant sequence
correct notation: c.6+8_6+9delAA |
G |
T |
A |
|
|
G |
| Note: If different deletions can lead to the same variant sequence, the deletion is entered as having occurred at the most 3' position possible. |
| reference sequence |
6+5 |
6+6 |
6+7 |
6+8 |
6+9 |
6+10 |
| G |
T |
A |
A |
A |
G |
variant sequence
incorrect notation: c.6+7_6+8delAA |
G |
T |
|
|
A |
G |
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| Syntax for Deletion of >20 Nucleotides in Exon |
| reference sequence |
1 |
2 |
3 |
4 |
... |
93 |
94 |
95 |
| A |
C |
T |
T |
... |
G |
C |
C |
variant sequence
correct notation: c.4_93del90 |
A |
C |
T |
|
|
|
C |
C |
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| Syntax for Deletion/Insertion |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
| A |
C |
T |
T |
T |
G |
T |
G |
C |
C |
variant sequence
correct notation: c.5_7delinsA |
A |
C |
T |
T |
|
|
A |
G |
C |
C |
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| Syntax for Insertion in Exon |
| reference sequence |
1 |
2 |
3 |
4 |
|
|
|
5 |
6 |
7 |
| A |
C |
T |
T |
|
|
|
G |
C |
C |
variant sequence
correct notation: c.4_5insTGT |
A |
C |
T |
T |
T |
G |
T |
G |
C |
C |
| Note: If different insertions can lead to the same variant sequence, the insertion is entered as having occurred at the most 3' position possible. |
| reference sequence |
1 |
2 |
3 |
|
|
|
4 |
5 |
6 |
7 |
| A |
C |
T |
|
|
|
T |
G |
C |
C |
variant sequence
incorrect notation: c.3_4insTTG |
A |
C |
T |
T |
T |
G |
T |
G |
C |
C |
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| Syntax for Insertion in Intron |
| reference sequence |
6+5 |
6+6 |
6+7 |
6+8 |
|
6+9 |
| G |
T |
A |
G |
|
G |
variant sequence
correct notation: c.6+8_6+9insA |
G |
T |
A |
G |
A |
G |
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| Syntax for Duplication of Single Nucleotide in Exon |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
|
6 |
7 |
8 |
9 |
10 |
| A |
C |
T |
T |
T |
|
G |
T |
G |
C |
C |
variant sequence
correct notation: c.5dupT |
A |
C |
T |
T |
T |
T |
G |
T |
G |
C |
C |
| Note: If an insertion can be described as a duplication, it has to be described as a duplication. |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
|
6 |
7 |
8 |
9 |
10 |
| A |
C |
T |
T |
T |
|
G |
T |
G |
C |
C |
variant sequence
incorrect notation: c.5_6insT |
A |
C |
T |
T |
T |
T |
G |
T |
G |
C |
C |
| Note: If different duplications can lead to the same variant sequence, the duplication is entered as having occurred at the most 3' position possible. |
| reference sequence |
1 |
2 |
3 |
4 |
|
5 |
6 |
7 |
8 |
9 |
10 |
| A |
C |
T |
T |
|
T |
G |
T |
G |
C |
C |
variant sequence
incorrect notation: c.4dupT |
A |
C |
T |
T |
T |
T |
G |
T |
G |
G |
C
C |
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| Syntax for Duplication of >1 but <=20 Nucleotides in Exon |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
|
|
9 |
10 |
| A |
C |
T |
T |
T |
G |
T |
G |
|
|
C |
C |
variant sequence
correct notation: c.7_8dupTG |
A |
C |
T |
T |
T |
G |
T |
G |
T |
G |
C |
C |
| Note: If an insertion can be described as a duplication, it has to be described as a duplication. |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
|
|
9 |
10 |
| A |
C |
T |
T |
T |
G |
T |
G |
|
|
C |
C |
variant sequence
incorrect notation: c.8_9insTG |
A |
C |
T |
T |
T |
G |
T |
G |
T |
G |
C |
C |
| Note: If different duplications can lead to the same variant sequence, the duplication is entered as having occurred at the most 3' position possible. |
| reference sequence |
1 |
2 |
3 |
4 |
5 |
6 |
7 |
|
|
8 |
9 |
10 |
| A |
C |
T |
T |
T |
G |
T |
|
|
G |
C |
C |
variant sequence
incorrect notation: c.6_7dupGT |
A |
C |
T |
T |
T |
G |
T |
G |
T |
G |
C |
C |
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