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: ENST00000642122
Querying Taster for transcript #2: ENST00000389048
Querying Taster for transcript #3: ENST00000618119
Querying Taster for transcript #4: ENST00000689605
MT speed 0.47 s - this script 2.862562 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
ENST00000618119	ALK	Benign	0\|100	3utr	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000389048(MANE Select)	ALK	Benign	1\|99	3utr	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000642122	ALK	Benign	3\|97	3utr	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000689605	CLIP4	Benign	11\|189	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD

MutationT@ster 2025

Variant:

2:29193179C>T_3_ENST00000618119

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Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 3utr
Tree vote: 0|100 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:29193179C>T (GRCh38)

Gene symbol

ALK

Gene constraints

LOEUF: 0.58, LOF (oe): 0.47, misssense (oe): 0.89, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000618119.4

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.4244G>A
g.728408G>A

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	rs186421480
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	418	418

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.432	0
	-0.927	0
(flanking)	1.355	0.886

?

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

2

Strand

-1

Original gDNA sequence snippet

TCCTTGGGATCCCTAAGACCGTGGAGGAGAGAGAGGCAATG

Altered gDNA sequence snippet

TCCTTGGGATCCCTAAGACCATGGAGGAGAGAGAGGCAATG

Original cDNA sequence snippet

TCCTTGGGATCCCTAAGACCGTGGAGGAGAGAGAGGCAATG

Altered cDNA sequence snippet

TCCTTGGGATCCCTAAGACCATGGAGGAGAGAGAGGCAATG

Wildtype AA sequence

MPTPGKHGWT VLQGRIGRPD NPFRVALEYI SSGNRSLSAV DFFALKNCSE GTSPGSKMAL
QSSFTCWNGT VLQLGQACDF HQDCAQGEDE SQMCRKLPVG FYCNFEDGFC GWTQGTLSPH
TPQWQVRTLK DARFQDHQDH ALLLSTTDVP ASESATVTSA TFPAPIKSSP CELRMSWLIR
GVLRGNVSLV LVENKTGKEQ GRMVWHVAAY EGLSLWQWMV LPLLDVSDRF WLQMVAWWGQ
GSRAIVAFDN ISISLDCYLT ISGEDKILQN TAPKSRNLFE RNPNKELKPG ENSPRQTPIF
DPTVHWLFTT CGASGPHGPT QAQCNNAYQN SNLSVEVGSE GPLKGIQIWK VPATDTYSIS
GYGAAGGKGG KNTMMRSHGV SVLGIFNLEK DDMLYILVGQ QGEDACPSTN QLIQKVCIGE
NNVIEEEIRV NRSVHEWAGG GGGGGGATYV FKMKDGVPVP LIIAAGGGGR AYGAKTDTFH
PERLENNSSV LGLNGNSGAA GGGGGWNDNT SLLWAGKSLQ EGATGGHSCP QAMKKWGWET
RGGFGGGGGG CSSGGGGGGY IGGNAASNND PEMDGEDGVS FISPLGILYT PALKVMEGHG
EVNIKHYLNC SHCEVDECHM DPESHKVICF CDHGTVLAED GVSCIVSPTP EPHLPLSLIL
SVVTSALVAA LVLAFSGIMI VYRRKHQELQ AMQMELQSPE YKLSKLRTST IMTDYNPNYC
FAGKTSSISD LKEVPRKNIT LIRGLGHGAF GEVYEGQVSG MPNDPSPLQV AVKTLPEVCS
EQDELDFLME ALIISKFNHQ NIVRCIGVSL QSLPRFILLE LMAGGDLKSF LRETRPRPSQ
PSSLAMLDLL HVARDIACGC QYLEENHFIH RDIAARNCLL TCPGPGRVAK IGDFGMARDI
YRASYYRKGG CAMLPVKWMP PEAFMEGIFT SKTDTWSFGV LLWEIFSLGY MPYPSKSNQE
VLEFVTSGGR MDPPKNCPGP VYRIMTQCWQ HQPEDRPNFA IILERIEYCT QDPDVINTAL
PIEYGPLVEE EEKVPVRPKD PEGVPPLLVS QQAKREEERS PAAPPPLPTT SSGKAAKKPT
AAEISVRVPR GPAVEGGHVN MAFSQSNPPS ELHKVHGSRN KPTSLWNPTY GSWFTEKPTK
KNNPIAKKEP HDRGNLGLEG SCTVPPNVAT GRLPGASLLL EPSSLTANMK EVPLFRLRHF
PCGNVNYGYQ QQGLPLEAAT APGAGHYEDT ILKSKNSMNQ PGP*

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

468 / 468

Last intron/exon boundary

3500

Theoretical NMD boundary in CDS

2982

Length of CDS

3732

Coding sequence (CDS) position

N/A

cDNA position

4244

gDNA position

728408

Chromosomal position

29193179

Speed

0.14 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:

2:29193179C>T_2_ENST00000389048

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 3utr
Tree vote: 1|99 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:29193179C>T (GRCh38)

Gene symbol

ALK

Gene constraints

LOEUF: 0.56, LOF (oe): 0.46, misssense (oe): 0.94, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000389048.8

Genbank transcript ID

NM_004304 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.5835G>A
g.728408G>A

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	rs186421480
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	418	418

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.432	0
	-0.927	0
(flanking)	1.355	0.886

?

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

2

Strand

-1

Original gDNA sequence snippet

TCCTTGGGATCCCTAAGACCGTGGAGGAGAGAGAGGCAATG

Altered gDNA sequence snippet

TCCTTGGGATCCCTAAGACCATGGAGGAGAGAGAGGCAATG

Original cDNA sequence snippet

TCCTTGGGATCCCTAAGACCGTGGAGGAGAGAGAGGCAATG

Altered cDNA sequence snippet

TCCTTGGGATCCCTAAGACCATGGAGGAGAGAGAGGCAATG

Wildtype AA sequence

MGAIGLLWLL PLLLSTAAVG SGMGTGQRAG SPAAGPPLQP REPLSYSRLQ RKSLAVDFVV
PSLFRVYARD LLLPPSSSEL KAGRPEARGS LALDCAPLLR LLGPAPGVSW TAGSPAPAEA
RTLSRVLKGG SVRKLRRAKQ LVLELGEEAI LEGCVGPPGE AAVGLLQFNL SELFSWWIRQ
GEGRLRIRLM PEKKASEVGR EGRLSAAIRA SQPRLLFQIF GTGHSSLESP TNMPSPSPDY
FTWNLTWIMK DSFPFLSHRS RYGLECSFDF PCELEYSPPL HDLRNQSWSW RRIPSEEASQ
MDLLDGPGAE RSKEMPRGSF LLLNTSADSK HTILSPWMRS SSEHCTLAVS VHRHLQPSGR
YIAQLLPHNE AAREILLMPT PGKHGWTVLQ GRIGRPDNPF RVALEYISSG NRSLSAVDFF
ALKNCSEGTS PGSKMALQSS FTCWNGTVLQ LGQACDFHQD CAQGEDESQM CRKLPVGFYC
NFEDGFCGWT QGTLSPHTPQ WQVRTLKDAR FQDHQDHALL LSTTDVPASE SATVTSATFP
APIKSSPCEL RMSWLIRGVL RGNVSLVLVE NKTGKEQGRM VWHVAAYEGL SLWQWMVLPL
LDVSDRFWLQ MVAWWGQGSR AIVAFDNISI SLDCYLTISG EDKILQNTAP KSRNLFERNP
NKELKPGENS PRQTPIFDPT VHWLFTTCGA SGPHGPTQAQ CNNAYQNSNL SVEVGSEGPL
KGIQIWKVPA TDTYSISGYG AAGGKGGKNT MMRSHGVSVL GIFNLEKDDM LYILVGQQGE
DACPSTNQLI QKVCIGENNV IEEEIRVNRS VHEWAGGGGG GGGATYVFKM KDGVPVPLII
AAGGGGRAYG AKTDTFHPER LENNSSVLGL NGNSGAAGGG GGWNDNTSLL WAGKSLQEGA
TGGHSCPQAM KKWGWETRGG FGGGGGGCSS GGGGGGYIGG NAASNNDPEM DGEDGVSFIS
PLGILYTPAL KVMEGHGEVN IKHYLNCSHC EVDECHMDPE SHKVICFCDH GTVLAEDGVS
CIVSPTPEPH LPLSLILSVV TSALVAALVL AFSGIMIVYR RKHQELQAMQ MELQSPEYKL
SKLRTSTIMT DYNPNYCFAG KTSSISDLKE VPRKNITLIR GLGHGAFGEV YEGQVSGMPN
DPSPLQVAVK TLPEVCSEQD ELDFLMEALI ISKFNHQNIV RCIGVSLQSL PRFILLELMA
GGDLKSFLRE TRPRPSQPSS LAMLDLLHVA RDIACGCQYL EENHFIHRDI AARNCLLTCP
GPGRVAKIGD FGMARDIYRA SYYRKGGCAM LPVKWMPPEA FMEGIFTSKT DTWSFGVLLW
EIFSLGYMPY PSKSNQEVLE FVTSGGRMDP PKNCPGPVYR IMTQCWQHQP EDRPNFAIIL
ERIEYCTQDP DVINTALPIE YGPLVEEEEK VPVRPKDPEG VPPLLVSQQA KREEERSPAA
PPPLPTTSSG KAAKKPTAAE ISVRVPRGPA VEGGHVNMAF SQSNPPSELH KVHGSRNKPT
SLWNPTYGSW FTEKPTKKNN PIAKKEPHDR GNLGLEGSCT VPPNVATGRL PGASLLLEPS
SLTANMKEVP LFRLRHFPCG NVNYGYQQQG LPLEAATAPG AGHYEDTILK SKNSMNQPGP
*

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

928 / 928

Last intron/exon boundary

5091

Theoretical NMD boundary in CDS

4113

Length of CDS

4863

Coding sequence (CDS) position

N/A

cDNA position

5835

gDNA position

728408

Chromosomal position

29193179

Speed

0.17 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:

2:29193179C>T_1_ENST00000642122

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 3utr
Tree vote: 3|97 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:29193179C>T (GRCh38)

Gene symbol

ALK

Gene constraints

LOEUF: 0.64, LOF (oe): 0.44, misssense (oe): 0.90, synonymous (oe): 1.12 ? (gnomAD)

Ensembl transcript ID

ENST00000642122.1

Genbank transcript ID

NM_001353765 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.2108G>A
g.728408G>A

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	rs186421480
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	418	418

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.432	0
	-0.927	0
(flanking)	1.355	0.886

?

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

2

Strand

-1

Original gDNA sequence snippet

TCCTTGGGATCCCTAAGACCGTGGAGGAGAGAGAGGCAATG

Altered gDNA sequence snippet

TCCTTGGGATCCCTAAGACCATGGAGGAGAGAGAGGCAATG

Original cDNA sequence snippet

TCCTTGGGATCCCTAAGACCGTGGAGGAGAGAGAGGCAATG

Altered cDNA sequence snippet

TCCTTGGGATCCCTAAGACCATGGAGGAGAGAGAGGCAATG

Wildtype AA sequence

MQMELQSPEY KLSKLRTSTI MTDYNPNYCF AGKTSSISDL KEVPRKNITL IRGLGHGAFG
EVYEGQVSGM PNDPSPLQVA VKTLPEVCSE QDELDFLMEA LIISKFNHQN IVRCIGVSLQ
SLPRFILLEL MAGGDLKSFL RETRPRPSQP SSLAMLDLLH VARDIACGCQ YLEENHFIHR
DIAARNCLLT CPGPGRVAKI GDFGMARDIY RASYYRKGGC AMLPVKWMPP EAFMEGIFTS
KTDTWSFGVL LWEIFSLGYM PYPSKSNQEV LEFVTSGGRM DPPKNCPGPV YRIMTQCWQH
QPEDRPNFAI ILERIEYCTQ DPDVINTALP IEYGPLVEEE EKVPVRPKDP EGVPPLLVSQ
QAKREEERSP AAPPPLPTTS SGKAAKKPTA AEISVRVPRG PAVEGGHVNM AFSQSNPPSE
LHKVHGSRNK PTSLWNPTYG SWFTEKPTKK NNPIAKKEPH DRGNLGLEGS CTVPPNVATG
RLPGASLLLE PSSLTANMKE VPLFRLRHFP CGNVNYGYQQ QGLPLEAATA PGAGHYEDTI
LKSKNSMNQP GP*

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

405 / 405

Last intron/exon boundary

1364

Theoretical NMD boundary in CDS

909

Length of CDS

1659

Coding sequence (CDS) position

N/A

cDNA position

2108

gDNA position

728408

Chromosomal position

29193179

Speed

0.14 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:

2:29193179C>T_4_ENST00000689605

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 11|189 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:29193179C>T (GRCh38)

Gene symbol

CLIP4

Gene constraints

LOEUF: 0.76, LOF (oe): 0.55, misssense (oe): 0.97, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000689605.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1923-3749C>T
g.95475C>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	rs186421480
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	418	418

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.432	0
	-0.927	0
(flanking)	1.355	0.886

?

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

2

Strand

1

Original gDNA sequence snippet

CATTGCCTCTCTCTCCTCCACGGTCTTAGGGATCCCAAGGA

Altered gDNA sequence snippet

CATTGCCTCTCTCTCCTCCATGGTCTTAGGGATCCCAAGGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTIEDLPDFP LEGNPLFGRY PFIFSASDTP VIFSISAAPM PSDCEFSFFD PNDASCQEIL
FDPKTSVSEL FAILRQWVPQ VQQNIDIIGN EILKRGCNVN DRDGLTDMTL LHYTCKSGAH
GIGDVETAVK FATQLIDLGA DISLRSRWTN MNALHYAAYF DVPELIRVIL KTSKPKDVDA
TCSDFNFGTA LHIAAYNLCA GAVKCLLEQG ANPAFRNDKG QIPADVVPDP VDMPLEMADA
AATAKEIKQM LLDAVPLSCN ISKAMLPNYD HVTGKAMLTS LGLKLGDRVV IAGQKVGTLR
FCGTTEFASG QWAGIELDEP EGKNNGSVGK VQYFKCAPKY GIFAPLSKIS KAKGRRKNIT
HTPSTKAAVP LIRSQKIDVA HVTSKVNTGL MTSKKDSASE STLSLPPGEE LKTVTEKDVA
LLGSVSSCSS TSSLEHRQSY PKKQNAISSN KKTMSKSPSL SSRASAGLNS SATSTANNSR
CEGELRLGER VLVVGQRLGT IRFFGTTNFA PGYWYGIELE KPHGKNDGSV GGVQYFSCSP
RYGIFAPPSR VQRVTDSLDT LSEISSNKQN HSYPGFRRSF STTSASSQKE INRRNAFSKS
KAALRRSWSS TPTAGGIEGS VKLHEGSQVL LTSSNEMGTV SPRVATNTLR VRTRLGPVYL
AYAAPC*

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

192 / 192

Last intron/exon boundary

2113

Theoretical NMD boundary in CDS

1871

Length of CDS

2001

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

95475

Chromosomal position

29193179

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