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: ENST00000579122
Querying Taster for transcript #2: ENST00000304494
Querying Taster for transcript #3: ENST00000579755
Querying Taster for transcript #4: ENST00000578845
Querying Taster for transcript #5: ENST00000530628
Querying Taster for transcript #6: ENST00000498124
Querying Taster for transcript #7: ENST00000498628
Querying Taster for transcript #8: ENST00000494262
Querying Taster for transcript #9: ENST00000479692
Querying Taster for transcript #10: ENST00000497750
MT speed 0.25 s - this script 2.699141 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000579122	CDKN2A	Deleterious	111\|89	without_aae	Yes	Single base exchange	N/A	Splice site changes
ENST00000578845	CDKN2A	Deleterious	135\|65	without_aae	No	Single base exchange	Normal
ENST00000498628	CDKN2A	Deleterious	135\|65	without_aae	No	Single base exchange	Normal
ENST00000494262	CDKN2A	Deleterious	135\|65	without_aae	No	Single base exchange	Normal
ENST00000579755(MANE Select)	CDKN2A	Benign	44\|56	3utr	No	Single base exchange	N/A
ENST00000530628	CDKN2A	Benign	59\|141	without_aae	Yes	Single base exchange	N/A	Splice site changes
ENST00000304494(MANE Select)	CDKN2A	Benign	89\|111	without_aae	No	Single base exchange	Normal
ENST00000497750	CDKN2A	Benign	89\|111	without_aae	No	Single base exchange	Normal
ENST00000479692	CDKN2A	Benign	92\|108	without_aae	No	Single base exchange	Normal
ENST00000498124	CDKN2A	Benign	97\|103	without_aae	No	Single base exchange	Normal

MutationT@ster 2025

Variant:

9:21970971G>A_1_ENST00000579122

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Splice site changes

Model: without_aae
Tree vote: 111|89 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21970971G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.06, LOF (oe): 0.50, misssense (oe): 1.29, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000579122.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.383+5C>T
g.24331C>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	rs1060501261
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.908	1
	3.036	1
(flanking)	2.466	1

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor weakened	24326	wt: 6.79 / mu: 6.66	-	wt: ATGTCGCACG\|gtacctgcgc mu: ATGTCGCACG\|gtacttgcgc

Distance from splice site

5

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

-1

Original gDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered gDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEPAAGSSME PSADWLATAA ARGRVEEVRA LLEAGALPNA PNSYGRRPIQ VMMMGSARVA
ELLLLHGAEP NCADPATLTR PVHDAAREGF LDTLVVLHRA GARLDVRDAW GRLPVDLAEE
LGHRDVARHP RLKEPERL*

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

32 / 32

Last intron/exon boundary

414

Theoretical NMD boundary in CDS

332

Length of CDS

417

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

24331

Chromosomal position

21970971

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

Back to summary table

MutationT@ster 2025

Variant:

9:21970971G>A_4_ENST00000578845

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Model: without_aae
Tree vote: 135|65 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21970971G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.30, LOF (oe): 0.42, misssense (oe): 1.24, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000578845.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.235C>T
g.24331C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1060501261
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.908	1
	3.036	1
(flanking)	2.466	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

9

Strand

-1

Original gDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered gDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Original cDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered cDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Wildtype AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SDIPD*

Mutated AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SDIPD*

Position of stopcodon in wt / mu CDS

318 / 318

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

106 / 106

Position of stopcodon in wt / mu cDNA

445 / 445

Position of start ATG in wt / mu cDNA

128 / 128

Last intron/exon boundary

431

Theoretical NMD boundary in CDS

253

Length of CDS

318

Coding sequence (CDS) position

235

cDNA position

362

gDNA position

24331

Chromosomal position

21970971

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

Back to summary table

MutationT@ster 2025

Variant:

9:21970971G>A_7_ENST00000498628

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Model: without_aae
Tree vote: 135|65 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21970971G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.30, LOF (oe): 0.42, misssense (oe): 1.24, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000498628.6

Genbank transcript ID

NM_001363763 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.235C>T
g.24331C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1060501261
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.908	1
	3.036	1
(flanking)	2.466	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

9

Strand

-1

Original gDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered gDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Original cDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered cDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Wildtype AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SDIPD*

Mutated AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SDIPD*

Position of stopcodon in wt / mu CDS

318 / 318

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

106 / 106

Position of stopcodon in wt / mu cDNA

802 / 802

Position of start ATG in wt / mu cDNA

485 / 485

Last intron/exon boundary

788

Theoretical NMD boundary in CDS

253

Length of CDS

318

Coding sequence (CDS) position

235

cDNA position

719

gDNA position

24331

Chromosomal position

21970971

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

Back to summary table

MutationT@ster 2025

Variant:

9:21970971G>A_8_ENST00000494262

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Model: without_aae
Tree vote: 135|65 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21970971G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.30, LOF (oe): 0.42, misssense (oe): 1.24, synonymous (oe): 1.27 ? (gnomAD)

Ensembl transcript ID

ENST00000494262.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.235C>T
g.24331C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1060501261
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.908	1
	3.036	1
(flanking)	2.466	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

9

Strand

-1

Original gDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered gDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Original cDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered cDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Wildtype AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SDIPD*

Mutated AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SDIPD*

Position of stopcodon in wt / mu CDS

318 / 318

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

106 / 106

Position of stopcodon in wt / mu cDNA

942 / 942

Position of start ATG in wt / mu cDNA

625 / 625

Last intron/exon boundary

928

Theoretical NMD boundary in CDS

253

Length of CDS

318

Coding sequence (CDS) position

235

cDNA position

859

gDNA position

24331

Chromosomal position

21970971

Speed

0.01 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

Back to summary table

MutationT@ster 2025

Variant:

9:21970971G>A_3_ENST00000579755

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 44|56 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21970971G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.50, LOF (oe): 0.81, misssense (oe): 1.16, synonymous (oe): 1.11 ? (gnomAD)

Ensembl transcript ID

ENST00000579755.2

Genbank transcript ID

NM_058195 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.492C>T
g.24331C>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	rs1060501261
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.908	1
	3.036	1
(flanking)	2.466	1

?

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

polyA signal ok

AA sequence altered

N/A

Chromosome

9

Strand

-1

Original gDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered gDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Original cDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered cDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Wildtype AA sequence

MVRRFLVTLR IRRACGPPRV RVFVVHIPRL TGEWAAPGAP AAVALVLMLL RSQRLGQQPL
PRRPGHDDGQ RPSGGAAAAP RRGAQLRRPR HSHPTRARRC PGGLPGHAGG AAPGRGAAGR
ARCLGPSARG PG*

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

62 / 62

Last intron/exon boundary

561

Theoretical NMD boundary in CDS

449

Length of CDS

399

Coding sequence (CDS) position

N/A

cDNA position

492

gDNA position

24331

Chromosomal position

21970971

Speed

0.12 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

Back to summary table

MutationT@ster 2025

Variant:

9:21970971G>A_5_ENST00000530628

Back to summary table

Prediction:

BenignPermalink

Summary:

Splice site changes

Model: without_aae
Tree vote: 59|141 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21970971G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.38, LOF (oe): 0.70, misssense (oe): 1.16, synonymous (oe): 1.11 ? (gnomAD)

Ensembl transcript ID

ENST00000530628.2

Genbank transcript ID

UniProt / AlphaMissense peptide

ARF_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.*27+5C>T
g.24331C>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	rs1060501261
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.908	1
	3.036	1
(flanking)	2.466	1

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor weakened	24326	wt: 6.79 / mu: 6.66	-	wt: ATGTCGCACG\|gtacctgcgc mu: ATGTCGCACG\|gtacttgcgc

Distance from splice site

5

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

-1

Original gDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered gDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVRRFLVTLR IRRACGPPRV RVFVVHIPRL TGEWAAPGAP AAVALVLMLL RSQRLGQQPL
PRRPGHDDGQ RPSGGAAAAP RRGAQLRRPR HSHPTRARRC PGGLPGHAGG AAPGRGAAGR
ARCLGPSARG PG*

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

81 / 81

Last intron/exon boundary

506

Theoretical NMD boundary in CDS

375

Length of CDS

399

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

24331

Chromosomal position

21970971

Speed

0.01 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

Back to summary table

MutationT@ster 2025

Variant:

9:21970971G>A_2_ENST00000304494

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 89|111 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21970971G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 0.79, LOF (oe): 0.31, misssense (oe): 1.25, synonymous (oe): 1.22 ? (gnomAD)

Ensembl transcript ID

ENST00000304494.10

Genbank transcript ID

NM_000077 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.388C>T
g.24331C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1060501261
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.908	1
	3.036	1
(flanking)	2.466	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

9

Strand

-1

Original gDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered gDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Original cDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered cDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Wildtype AA sequence

MEPAAGSSME PSADWLATAA ARGRVEEVRA LLEAGALPNA PNSYGRRPIQ VMMMGSARVA
ELLLLHGAEP NCADPATLTR PVHDAAREGF LDTLVVLHRA GARLDVRDAW GRLPVDLAEE
LGHRDVARYL RAAAGGTRGS NHARIDAAEG PSDIPD*

Mutated AA sequence

MEPAAGSSME PSADWLATAA ARGRVEEVRA LLEAGALPNA PNSYGRRPIQ VMMMGSARVA
ELLLLHGAEP NCADPATLTR PVHDAAREGF LDTLVVLHRA GARLDVRDAW GRLPVDLAEE
LGHRDVARYL RAAAGGTRGS NHARIDAAEG PSDIPD*

Position of stopcodon in wt / mu CDS

471 / 471

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

157 / 157

Position of stopcodon in wt / mu cDNA

501 / 501

Position of start ATG in wt / mu cDNA

31 / 31

Last intron/exon boundary

487

Theoretical NMD boundary in CDS

406

Length of CDS

471

Coding sequence (CDS) position

388

cDNA position

418

gDNA position

24331

Chromosomal position

21970971

Speed

0.01 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

Back to summary table

MutationT@ster 2025

Variant:

9:21970971G>A_10_ENST00000497750

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 89|111 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21970971G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.85, LOF (oe): 0.00, misssense (oe): 1.26, synonymous (oe): 1.23 ? (gnomAD)

Ensembl transcript ID

ENST00000497750.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.235C>T
g.24331C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1060501261
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.908	1
	3.036	1
(flanking)	2.466	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

9

Strand

-1

Original gDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered gDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Original cDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered cDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Wildtype AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SGED*

Mutated AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SGED*

Position of stopcodon in wt / mu CDS

315 / 315

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

105 / 105

Position of stopcodon in wt / mu cDNA

390 / 390

Position of start ATG in wt / mu cDNA

76 / 76

Last intron/exon boundary

72

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

315

Coding sequence (CDS) position

235

cDNA position

310

gDNA position

24331

Chromosomal position

21970971

Speed

0.01 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:

9:21970971G>A_9_ENST00000479692

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 92|108 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21970971G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.62, LOF (oe): 0.57, misssense (oe): 1.27, synonymous (oe): 1.25 ? (gnomAD)

Ensembl transcript ID

ENST00000479692.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.235C>T
g.24331C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1060501261
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.908	1
	3.036	1
(flanking)	2.466	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

9

Strand

-1

Original gDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered gDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Original cDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered cDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Wildtype AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SVTASIQVPG GEEGDFGSSY
S*

Mutated AA sequence

MMMGSARVAE LLLLHGAEPN CADPATLTRP VHDAAREGFL DTLVVLHRAG ARLDVRDAWG
RLPVDLAEEL GHRDVARYLR AAAGGTRGSN HARIDAAEGP SVTASIQVPG GEEGDFGSSY
S*

Position of stopcodon in wt / mu CDS

366 / 366

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

122 / 122

Position of stopcodon in wt / mu cDNA

381 / 381

Position of start ATG in wt / mu cDNA

16 / 16

Last intron/exon boundary

319

Theoretical NMD boundary in CDS

253

Length of CDS

366

Coding sequence (CDS) position

235

cDNA position

250

gDNA position

24331

Chromosomal position

21970971

Speed

0.01 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:

9:21970971G>A_6_ENST00000498124

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 97|103 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:21970971G>A (GRCh38)

Gene symbol

CDKN2A

Gene constraints

LOEUF: 1.03, LOF (oe): 0.52, misssense (oe): 1.24, synonymous (oe): 1.25 ? (gnomAD)

Ensembl transcript ID

ENST00000498124.1

Genbank transcript ID

NM_001195132 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.388C>T
g.24331C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1060501261
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.908	1
	3.036	1
(flanking)	2.466	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

9

Strand

-1

Original gDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered gDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Original cDNA sequence snippet

ATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGC

Altered cDNA sequence snippet

ATCGCGATGTCGCACGGTACTTGCGCGCGGCTGCGGGGGGC

Wildtype AA sequence

MEPAAGSSME PSADWLATAA ARGRVEEVRA LLEAGALPNA PNSYGRRPIQ VMMMGSARVA
ELLLLHGAEP NCADPATLTR PVHDAAREGF LDTLVVLHRA GARLDVRDAW GRLPVDLAEE
LGHRDVARYL RAAAGGTRGS NHARIDAAEG PSEMIGNHLW VCRSRHA*

Mutated AA sequence

MEPAAGSSME PSADWLATAA ARGRVEEVRA LLEAGALPNA PNSYGRRPIQ VMMMGSARVA
ELLLLHGAEP NCADPATLTR PVHDAAREGF LDTLVVLHRA GARLDVRDAW GRLPVDLAEE
LGHRDVARYL RAAAGGTRGS NHARIDAAEG PSEMIGNHLW VCRSRHA*

Position of stopcodon in wt / mu CDS

504 / 504

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

168 / 168

Position of stopcodon in wt / mu cDNA

543 / 543

Position of start ATG in wt / mu cDNA

40 / 40

Last intron/exon boundary

693

Theoretical NMD boundary in CDS

603

Length of CDS

504

Coding sequence (CDS) position

388

cDNA position

427

gDNA position

24331

Chromosomal position

21970971

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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