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: ENST00000423902
Querying Taster for transcript #2: ENST00000524602
Querying Taster for transcript #3: ENST00000525508
MT speed 0.08 s - this script 2.447694 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length
ENST00000524602	CHD7	Deleterious	119\|81	without_aae	No	Single base exchange	N/A
ENST00000423902(MANE Select)	CHD7	Benign	41\|159	without_aae	No	Single base exchange	N/A
ENST00000525508	CHD7	Benign	52\|148	without_aae	No	Single base exchange	N/A

MutationT@ster 2025

Variant:

8:60780977C>T_2_ENST00000524602

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Prediction:

DeleteriousPermalink

Summary:

Model: without_aae
Tree vote: 119|81 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr8:60780977C>T (GRCh38)

Gene symbol

CHD7

Gene constraints

LOEUF: 0.28, LOF (oe): 0.18, misssense (oe): 0.91, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000524602.5

Genbank transcript ID

NM_001316690 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1666-23C>T
g.102238C>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	rs45505899
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	361	361

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.092	1
	2.374	1
(flanking)	1.673	0.997

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

23

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

8

Strand

1

Original gDNA sequence snippet

GAAGAATGATAAACTAATTTCAATTCCTATTTGTGTCTCTC

Altered gDNA sequence snippet

GAAGAATGATAAACTAATTTTAATTCCTATTTGTGTCTCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MADPGMMSLF GEDGNIFSEG LEGLGECGYP ENPVNPMGQQ MPIDQGFASL QPSLHHPSTN
QNQTKLTHFD HYNQYEQQKM HLMDQPNRMM SNTPGNGLAS PHSQYHTPPV PQVPHGGSGG
GQMGVYPGMQ NERHGQSFVD SSSMWGPRAV QVPDQIRAPY QQQQPQPQPP QPAPSGPPAQ
GHPQHMQQMG SYMARGDFSM QQHGQPQQRM SQFSQGQEGL NQGNPFIATS GPGHLSHVPQ
QSPSMAPSLR HSVQQFHHHP STALHGESVA HSPRFSPNPP QQGAVRPQTL NFSSRSQTVP
SPTINNSGQY SRYPYSNLNQ GLVNNTGMNQ NLGLTNNTPM NQSVPRYPNA VGFPSNSGQG
LMHQQPIHPS GSLNQMNTQT MHPSQPQGTY ASPPPMSPMK AMSNPAGTPP PQVRPGSAGI
PMEVGSYPNM PHPQPSHQPP GAMGIGQRNM GPRNMQQSRP FIGMSSAPRE LTGHMRPNGC
PGVGLGDPQA IQERLIPGQQ HPGQQPSFQQ LPTCPPLQPH PGLHHQSSPP HPHHQPWAQL
HPSPQNTPQK VPVHQHSPSE PFLEKPVPDM TQKPKQKRHR CRNPNKLDIN TLTGEERVPV
VNKRNGKKMG GAMAPPMKDL PRWLEENPEF AVAPDWTDIV KQSGFVPESM FDRLLTGPVV
RGEGASRRGR RPKSEIARAA AAAAAVASTS GINPLLVNSL FAGMDLTSLQ NLQNLQSLQL
AGLMGFPPGL ATAATAGGDA KNPAAVLPLM LPGMAGLPNV FGLGGLLNNP LSAATGNTTT
ASSQGEPEDS TSKGEEKGNE NEDENKDSEK STDAVSAADS ANGSVGAATA PAGLPSNPLA
FNPFLLSTMA PGLFYPSMFL PPGLGGLTLP GFPALAGLQN AVGSSEEKAA DKAEGGPFKD
GETLEGSDAE ESLDKTAESS LLEDEIAQGE ELDSLDGGDE IENNENDE*

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

69 / 69

Last intron/exon boundary

1997

Theoretical NMD boundary in CDS

1878

Length of CDS

2847

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

102238

Chromosomal position

60780977

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:

8:60780977C>T_1_ENST00000423902

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 41|159 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr8:60780977C>T (GRCh38)

Gene symbol

CHD7

Gene constraints

LOEUF: 0.11, LOF (oe): 0.07, misssense (oe): 0.82, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000423902.7

Genbank transcript ID

NM_017780 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1666-23C>T
g.102238C>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	rs45505899
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	361	361

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.092	1
	2.374	1
(flanking)	1.673	0.997

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

23

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

8

Strand

1

Original gDNA sequence snippet

GAAGAATGATAAACTAATTTCAATTCCTATTTGTGTCTCTC

Altered gDNA sequence snippet

GAAGAATGATAAACTAATTTTAATTCCTATTTGTGTCTCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MADPGMMSLF GEDGNIFSEG LEGLGECGYP ENPVNPMGQQ MPIDQGFASL QPSLHHPSTN
QNQTKLTHFD HYNQYEQQKM HLMDQPNRMM SNTPGNGLAS PHSQYHTPPV PQVPHGGSGG
GQMGVYPGMQ NERHGQSFVD SSSMWGPRAV QVPDQIRAPY QQQQPQPQPP QPAPSGPPAQ
GHPQHMQQMG SYMARGDFSM QQHGQPQQRM SQFSQGQEGL NQGNPFIATS GPGHLSHVPQ
QSPSMAPSLR HSVQQFHHHP STALHGESVA HSPRFSPNPP QQGAVRPQTL NFSSRSQTVP
SPTINNSGQY SRYPYSNLNQ GLVNNTGMNQ NLGLTNNTPM NQSVPRYPNA VGFPSNSGQG
LMHQQPIHPS GSLNQMNTQT MHPSQPQGTY ASPPPMSPMK AMSNPAGTPP PQVRPGSAGI
PMEVGSYPNM PHPQPSHQPP GAMGIGQRNM GPRNMQQSRP FIGMSSAPRE LTGHMRPNGC
PGVGLGDPQA IQERLIPGQQ HPGQQPSFQQ LPTCPPLQPH PGLHHQSSPP HPHHQPWAQL
HPSPQNTPQK VPVHQHSPSE PFLEKPVPDM TQVSGPNAQL VKSDDYLPSI EQQPQQKKKK
KKNNHIVAED PSKGFGKDDF PGGVDNQELN RNSLDGSQEE KKKKKRSKAK KDPKEPKEPK
EKKEPKEPKT PKAPKIPKEP KEKKAKTATP KPKSSKKSSN KKPDSEASAL KKKVNKGKTE
GSENSDLDKT PPPSPPPEED EDPGVQKRRS SRQVKRKRYT EDLEFKISDE EADDADAAGR
DSPSNTSQSE QQESVDAEGP VVEKIMSSRS VKKQKESGEE VEIEEFYVKY KNFSYLHCQW
ASIEDLEKDK RIQQKIKRFK AKQGQNKFLS EIEDELFNPD YVEVDRIMDF ARSTDDRGEP
VTHYLVKWCS LPYEDSTWER RQDIDQAKIE EFEKLMSREP ETERVERPPA DDWKKSESSR
EYKNNNKLRE YQLEGVNWLL FNWYNMRNCI LADEMGLGKT IQSITFLYEI YLKGIHGPFL
VIAPLSTIPN WEREFRTWTE LNVVVYHGSQ ASRRTIQLYE MYFKDPQGRV IKGSYKFHAI
ITTFEMILTD CPELRNIPWR CVVIDEAHRL KNRNCKLLEG LKMMDLEHKV LLTGTPLQNT
VEELFSLLHF LEPSRFPSET TFMQEFGDLK TEEQVQKLQA ILKPMMLRRL KEDVEKNLAP
KEETIIEVEL TNIQKKYYRA ILEKNFTFLS KGGGQANVPN LLNTMMELRK CCNHPYLING
AEEKILEEFK ETHNAESPDF QLQAMIQAAG KLVLIDKLLP KLKAGGHRVL IFSQMVRCLD
ILEDYLIQRR YPYERIDGRV RGNLRQAAID RFSKPDSDRF VFLLCTRAGG LGINLTAADT
CIIFDSDWNP QNDLQAQARC HRIGQSKSVK IYRLITRNSY EREMFDKASL KLGLDKAVLQ
SMSGRENATN GVQQLSKKEI EDLLRKGAYG ALMDEEDEGS KFCEEDIDQI LLRRTHTITI
ESEGKGSTFA KASFVASGNR TDISLDDPNF WQKWAKKAEL DIDALNGRNN LVIDTPRVRK
QTRLYSAVKE DELMEFSDLE SDSEEKPCAK PRRPQDKSQG YARSECFRVE KNLLVYGWGR
WTDILSHGRY KRQLTEQDVE TICRTILVYC LNHYKGDENI KSFIWDLITP TADGQTRALV
NHSGLSAPVP RGRKGKKVKA QSTQPVVQDA DWLASCNPDA LFQEDSYKKH LKHHCNKVLL
RVRMLYYLRQ EVIGDQADKI LEGADSSEAD VWIPEPFHAE VPADWWDKEA DKSLLIGVFK
HGYEKYNSMR ADPALCFLER VGMPDAKAIA AEQRGTDMLA DGGDGGEFDR EDEDPEYKPT
RTPFKDEIDE FANSPSEDKE ESMEIHATGK HSESNAELGQ LYWPNTSTLT TRLRRLITAY
QRSYKRQQMR QEALMKTDRR RRRPREEVRA LEAEREAIIS EKRQKWTRRE EADFYRVVST
FGVIFDPVKQ QFDWNQFRAF ARLDKKSDES LEKYFSCFVA MCRRVCRMPV KPDDEPPDLS
SIIEPITEER ASRTLYRIEL LRKIREQVLH HPQLGERLKL CQPSLDLPEW WECGRHDRDL
LVGAAKHGVS RTDYHILNDP ELSFLDAHKN FAQNRGAGNT SSLNPLAVGF VQTPPVISSA
HIQDERVLEQ AEGKVEEPEN PAAKEKCEGK EEEEETDGSG KESKQECEAE ASSVKNELKG
VEVGADTGSK SISEKGSEED EEEKLEDDDK SEESSQPEAG AVSRGKNFDE ESNASMSTAR
DETRDGFYME DGDPSVAQLL HERTFAFSFW PKDRVMINRL DNICEAVLKG KWPVNRRQMF
DFQGLIPGYT PTTVDSPLQK RSFAELSMVG QASISGSEDI TTSPQLSKED ALNLSVPRQR
RRRRRKIEIE AERAAKRRNL MEMVAQLRES QVVSENGQEK VVDLSKASRE ATSSTSNFSS
LSSKFILPNV STPVSDAFKT QMELLQAGLS RTPTRHLLNG SLVDGEPPMK RRRGRRKNVE
GLDLLFMSHK RTSLSAEDAE VTKAFEEDIE TPPTRNIPSP GQLDPDTRIP VINLEDGTRL
VGEDAPKNKD LVEWLKLHPT YTVDMPSYVP KNADVLFSSF QKPKQKRHRC RNPNKLDINT
LTGEERVPVV NKRNGKKMGG AMAPPMKDLP RWLEENPEFA VAPDWTDIVK QSGFVPESMF
DRLLTGPVVR GEGASRRGRR PKSEIARAAA AAAAVASTSG INPLLVNSLF AGMDLTSLQN
LQNLQSLQLA GLMGFPPGLA TAATAGGDAK NPAAVLPLML PGMAGLPNVF GLGGLLNNPL
SAATGNTTTA SSQGEPEDST SKGEEKGNEN EDENKDSEKS TDAVSAADSA NGSVGAATAP
AGLPSNPLAF NPFLLSTMAP GLFYPSMFLP PGLGGLTLPG FPALAGLQNA VGSSEEKAAD
KAEGGPFKDG ETLEGSDAEE SLDKTAESSL LEDEIAQGEE LDSLDGGDEI ENNENDE*

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

518 / 518

Last intron/exon boundary

8593

Theoretical NMD boundary in CDS

8025

Length of CDS

8994

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

102238

Chromosomal position

60780977

Speed

0.04 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:

8:60780977C>T_3_ENST00000525508

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 52|148 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr8:60780977C>T (GRCh38)

Gene symbol

CHD7

Gene constraints

LOEUF: 0.08, LOF (oe): 0.03, misssense (oe): 0.88, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000525508.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1666-23C>T
g.102238C>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	rs45505899
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	361	361

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.092	1
	2.374	1
(flanking)	1.673	0.997

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

23

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

8

Strand

1

Original gDNA sequence snippet

GAAGAATGATAAACTAATTTCAATTCCTATTTGTGTCTCTC

Altered gDNA sequence snippet

GAAGAATGATAAACTAATTTTAATTCCTATTTGTGTCTCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MADPGMMSLF GEDGNIFSEG LEGLGECGYP ENPVNPMGQQ MPIDQGFASL QPSLHHPSTN
QNQTKLTHFD HYNQYEQQKM HLMDQPNRMM SNTPGNGLAS PHSQYHTPPV PQVPHGGSGG
GQMGVYPGMQ NERHGQSFVD SSSMWGPRAV QVPDQIRAPY QQQQPQPQPP QPAPSGPPAQ
GHPQHMQQMG SYMARGDFSM QQHGQPQQRM SQFSQGQEGL NQGNPFIATS GPGHLSHVPQ
QSPSMAPSLR HSVQQFHHHP STALHGESVA HSPRFSPNPP QQGAVRPQTL NFSSRSQTVP
SPTINNSGQY SRYPYSNLNQ GLVNNTGMNQ NLGLTNNTPM NQSVPRYPNA VGFPSNSGQG
LMHQQPIHPS GSLNQMNTQT MHPSQPQGTY ASPPPMSPMK AMSNPAGTPP PQVRPGSAGI
PMEVGSYPNM PHPQPSHQPP GAMGIGQRNM GPRNMQQSRP FIGMSSAPRE LTGHMRPNGC
PGVGLGDPQA IQERLIPGQQ HPGQQPSFQQ LPTCPPLQPH PGLHHQSSPP HPHHQPWAQL
HPSPQNTPQK VPVHQHSPSE PFLEKPVPDM TQVSGPNAQL VKSDDYLPSI EQQPQQKKKK
KKNNHIVAED PSKGFGKDDF PGGVDNQELN RNSLDGSQEE KKKKKRSKAK KDPKEPKEPK
EKKEPKEPKT PKAPKIPKEP KEKKAKTATP KPKSSKKSSN KKPDSEASAL KKKVNKGKTE
GSENSDLDKT PPPSPPPEED EDPGVQKRRS SRQVKRKRYT EDLEFKISDE EADDADAAGR
DSPSNTSQSE QQESVDAEGP VVEKIMSSRS VKKQKESGEE VEIEEFYVKY KNFSYLHCQW
ASIEDLEKDK RIQQKIKRFK AKQGQNKFLS EIEDELFNPD YVEVDRIMDF ARSTDDRGEP
VTHYLVKWCS LPYEDSTWER RQDIDQAKIE EFEKLMSREP ETERVERPPA DDWKKSESSR
EYKNNNKLRE YQLEGVNWLL FNWYNMRNCI LADEMGLGKT IQSITFLYEI YLKGIHGPFL
VIAPLSTIPN WEREFRTWTE LNVVVYHGSQ ASRRTIQLYE MYFKDPQGRV IKGSYKFHAI
ITTFEMILTD CPELRNIPWR CVVIDEAHRL KNRNCKLLEG LKMMDLVSDH IGDCTEPE*

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

1 / 1

Last intron/exon boundary

3201

Theoretical NMD boundary in CDS

3150

Length of CDS

3417

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

102238

Chromosomal position

60780977

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