Table 1 Genome annotation of the SHANK3 guanine duplication (rs797044936).

From: A recurrent SHANK3 frameshift variant in Autism Spectrum Disorder

Reference genome

Transcript accession

Exon

Genomic position

Coding change

Protein change

Annotation tool

Hg38

NM_033517.1

21

Chr22:50721512–50721513

c.3679dup

p.(Ala1227Glyfs*69)

1Alamut Visual v2.15.0

2NM_001080420.1

22

Chr22:g.50721512dup

c.3727dup

p.(Ala1243Glyfs*69)

Alamut Visual v2.15.0

ENST00000262795.5

24

Chr22:g.50721512dup

c.3676dup

p.(Ala1226Glyfs*69)

Alamut Visual v2.15.0

NM_001372044 (replaced NM_033517)

22

22-50721503-50721504-T-TG

c.3855dupG

p.L1285fs

MSSNG

Hg19

NM_033517.1

21

Chr22:51159940–51159941

c.3679dup

p.(Ala1227Glyfs*69)

Alamut Visual v2.15.0

NM_001080420.1

22

Chr22:g.51159940dup

c.3727dup

p.(Ala1243Glyfs*69)

Alamut Visual v2.15.0

ENST00000262795.5

24

Chr22:g.51159940dup

c.3676dup

p.(Ala1226Glyfs*69)

Alamut Visual v2.15.0

NM_033517

21

chr22:51159932-51159932-T-TG

c.3630dup

p.L1210fs

VariCarta; GATK VariCarta

chr22:51159933-51159933-G-GG

ENST00000262795.3

22

22-5119932-T-TG

c.3719_3720 insG

p.Ala1243GlyfsTer6

O’Roak et al.40.

ENST00000262795.3

22

22-5119932-T-TG

c.3720dupG

p.L1240fs

Feliciano et al.41.

  1. The annotation considers different reference genomes, the position of the duplication in the guanine string, and the annotation tool. The guanine duplication in each carrier in the main text of the paper is referred to as p.Ala1227Glyfs*69.
  2. 1Alamut Visual version 2.15 (SOPHiA GENETICS, Lausanne, Switzerland). This tool annotates the final G as duplicated and provides the coding and protein change as well as ClinVar entries and general population frequencies (Supplementary Fig. S3).
  3. 2NM_001080420.1 record has been removed from NCBI. This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein. Exon 11 was based on ab initio prediction and is not supported by transcript data.
  4. At the time of submission, the most recent RefSeq NM_01372044, which replaces and updates NM_033517, was not available in the Alamut software.
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