MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000695541
Querying Taster for transcript #2: ENST00000481781
Querying Taster for transcript #3: ENST00000643349
Querying Taster for transcript #4: ENST00000397270
MT speed 0.06 s - this script 2.387598 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000695541	IGF2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000481781	IGF2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000397270	INS-IGF2	Benign	2\|198	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

Some transcripts had annotation problems and are not shown

MutationT@ster 2025

Variant:

11:2148654C>A_1_ENST00000695541

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr11:2148654C>A (GRCh38)

Gene symbol

IGF2

Gene constraints

no data

Ensembl transcript ID

ENST00000695541.1

Genbank transcript ID

NM_001007139 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-249+472G>T
g.9738G>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3741205
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.232	0
	-0.869	0
(flanking)	-0.699	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

11

Strand

-1

Original gDNA sequence snippet

GCCCGAGATTCTGGCGCAGAGATTTTATTTATACATATATA

Altered gDNA sequence snippet

GCCCGAGATTCTGGCGCAGATATTTTATTTATACATATATA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MGIPMGKSML VLLTFLAFAS CCIAAYRPSE TLCGGELVDT LQFVCGDRGF YFSRPASRVS
RRSRGIVEEC CFRSCDLALL ETYCATPAKS ERDVSTPPTV LPDNFPRYPV GKFFQYDTWK
QSTQRLRRGL PALLRARRGH VLAKELEAFR EAKRHRPLIA LPTQDPAHGG APPEMASNRK
*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

577 / 577

Last intron/exon boundary

882

Theoretical NMD boundary in CDS

255

Length of CDS

543

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

9738

Chromosomal position

2148654

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

11:2148654C>A_2_ENST00000481781

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr11:2148654C>A (GRCh38)

Gene symbol

IGF2

Gene constraints

no data

Ensembl transcript ID

ENST00000481781.3

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-249+472G>T
g.9738G>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3741205
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.232	0
	-0.869	0
(flanking)	-0.699	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

11

Strand

-1

Original gDNA sequence snippet

GCCCGAGATTCTGGCGCAGAGATTTTATTTATACATATATA

Altered gDNA sequence snippet

GCCCGAGATTCTGGCGCAGATATTTTATTTATACATATATA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MGIPMGKSML VLLTFLAFAS CCIAAYRPSE TLCGGELVDT LQFVCGDRGF YFSRPASRVS
RRSRGIVEEC CFRSCDLALL ETYCATPAKS ERDVSTPPTV LPDNFPRYPV GKFFQYDTWK
QSTQRLRRGL PALLRARRGH VLAKELEAFR EAKRHRPLIA LPTQDPAHGG APPEMASNRK
*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

594 / 594

Last intron/exon boundary

899

Theoretical NMD boundary in CDS

255

Length of CDS

543

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

9738

Chromosomal position

2148654

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

11:2148654C>A_4_ENST00000397270

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 2|198 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr11:2148654C>A (GRCh38)

Gene symbol

INS-IGF2

Gene constraints

LOEUF: 1.44, LOF (oe): 0.95, misssense (oe): 0.94, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000397270.1

Genbank transcript ID

NM_001042376 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.407+472G>T
g.12556G>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3741205
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.232	0
	-0.869	0
(flanking)	-0.699	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

11

Strand

-1

Original gDNA sequence snippet

GCCCGAGATTCTGGCGCAGAGATTTTATTTATACATATATA

Altered gDNA sequence snippet

GCCCGAGATTCTGGCGCAGATATTTTATTTATACATATATA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MALWMRLLPL LALLALWGPD PAAAFVNQHL CGSHLVEALY LVCGERGFFY TPKTRREAED
LQASALSLSS STSTWPEGLD ATARAPPALV VTANIGQAGG SSSRQFRQRA LGTSDSPVLF
IHCPGAAGTA QGLEYRGRRV TTELVWEEVD SSPQPQGSES LPAQPPAQPA PQPEPQQARE
PSPEVSCCGL WPRRPQRSQN *

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

60 / 60

Last intron/exon boundary

708

Theoretical NMD boundary in CDS

598

Length of CDS

603

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

12556

Chromosomal position

2148654

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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Problem:

1

MutationT@ster 2025

Data problem

No NCBI gene ID found.

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