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: ENST00000645635
Querying Taster for transcript #2: ENST00000394634
Querying Taster for transcript #3: ENST00000394635
Querying Taster for transcript #4: ENST00000512148
Querying Taster for transcript #5: ENST00000510800
MT speed 0.17 s - this script 2.541092 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
ENST00000510800	CFI	Benign	25\|75	3utr	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000394634(MANE Select)	CFI	Benign	171\|29	without_aae	Yes	Single base exchange	N/A	Homozygous in gnomAD Splice site changes
ENST00000394635	CFI	Benign	171\|29	without_aae	Yes	Single base exchange	N/A	Homozygous in gnomAD Splice site changes
ENST00000512148	CFI	Benign	171\|29	without_aae	Yes	Single base exchange	N/A	Homozygous in gnomAD Splice site changes

Some transcripts had annotation problems and are not shown

MutationT@ster 2025

Variant:

4:109764531G>A_5_ENST00000510800

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 3utr
Tree vote: 25|75 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr4:109764531G>A (GRCh38)

Gene symbol

CFI

Gene constraints

LOEUF: 1.66, LOF (oe): 1.11, misssense (oe): 0.89, synonymous (oe): 0.88 ? (gnomAD)

Ensembl transcript ID

ENST00000510800.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.495C>T
g.37620C>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	rs79375065
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	491	14037	14528

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.74	0
	0.452	0.118
(flanking)	4.84	0.998

?

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

4

Strand

-1

Original gDNA sequence snippet

CCTTGGGTTTCAACAGTGAGCGCTTGTATCAGTGGATTTTC

Altered gDNA sequence snippet

CCTTGGGTTTCAACAGTGAGTGCTTGTATCAGTGGATTTTC

Original cDNA sequence snippet

CCTTGGGTTTCAACAGTGAGCGCTTGTATCAGTGGATTTTC

Altered cDNA sequence snippet

CCTTGGGTTTCAACAGTGAGTGCTTGTATCAGTGGATTTTC

Wildtype AA sequence

MKLLHVFLLF LCFHLRFCKV TYTSQEDLVE KKCLAKKYTH LSCDKVFCQP WQRCIEGTCV
CKLPYQCPKN GTAVCATNRR SFPTYCQQKS LECLHPGTKF LNNGTCTAEG KFSVSLKHGN
TDSEGIVEVK LVDQDKTMFI CKSSWSMREA NVACLDLGFQ Q*

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

8 / 8

Last intron/exon boundary

335

Theoretical NMD boundary in CDS

277

Length of CDS

486

Coding sequence (CDS) position

N/A

cDNA position

495

gDNA position

37620

Chromosomal position

109764531

Speed

0.13 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:

4:109764531G>A_2_ENST00000394634

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Splice site changes

Model: without_aae
Tree vote: 171|29 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr4:109764531G>A (GRCh38)

Gene symbol

CFI

Gene constraints

LOEUF: 1.08, LOF (oe): 0.85, misssense (oe): 0.97, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000394634.7

Genbank transcript ID

NM_000204 (exact from MANE), NM_001375281 (by similarity), NM_001375279 (by similarity), NM_001375284 (by similarity)

UniProt / AlphaMissense peptide

CFAI_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.482+6C>T
g.37620C>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	rs79375065
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	491	14037	14528

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.74	0
	0.452	0.118
(flanking)	4.84	0.998

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor weakened	37614	wt: 4.69 / mu: 8.34	-	wt: GGTTTCAACA\|gtgagcgctt mu: GGTTTCAACA\|gtgagtgctt

Distance from splice site

6

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

4

Strand

-1

Original gDNA sequence snippet

CCTTGGGTTTCAACAGTGAGCGCTTGTATCAGTGGATTTTC

Altered gDNA sequence snippet

CCTTGGGTTTCAACAGTGAGTGCTTGTATCAGTGGATTTTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MKLLHVFLLF LCFHLRFCKV TYTSQEDLVE KKCLAKKYTH LSCDKVFCQP WQRCIEGTCV
CKLPYQCPKN GTAVCATNRR SFPTYCQQKS LECLHPGTKF LNNGTCTAEG KFSVSLKHGN
TDSEGIVEVK LVDQDKTMFI CKSSWSMREA NVACLDLGFQ QGADTQRRFK LSDLSINSTE
CLHVHCRGLE TSLAECTFTK RRTMGYQDFA DVVCYTQKAD SPMDDFFQCV NGKYISQMKA
CDGINDCGDQ SDELCCKACQ GKGFHCKSGV CIPSQYQCNG EVDCITGEDE VGCAGFASVT
QEETEILTAD MDAERRRIKS LLPKLSCGVK NRMHIRRKRI VGGKRAQLGD LPWQVAIKDA
SGITCGGIYI GGCWILTAAH CLRASKTHRY QIWTTVVDWI HPDLKRIVIE YVDRIIFHEN
YNAGTYQNDI ALIEMKKDGN KKDCELPRSI PACVPWSPYL FQPNDTCIVS GWGREKDNER
VFSLQWGEVK LISNCSKFYG NRFYEKEMEC AGTYDGSIDA CKGDSGGPLV CMDANNVTYV
WGVVSWGENC GKPEFPGVYT KVANYFDWIS YHVGRPFISQ YNV*

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

29 / 29

Last intron/exon boundary

1562

Theoretical NMD boundary in CDS

1483

Length of CDS

1752

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

37620

Chromosomal position

109764531

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:

4:109764531G>A_3_ENST00000394635

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Splice site changes

Model: without_aae
Tree vote: 171|29 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr4:109764531G>A (GRCh38)

Gene symbol

CFI

Gene constraints

LOEUF: 1.08, LOF (oe): 0.85, misssense (oe): 0.97, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000394635.8

Genbank transcript ID

NM_001375278 (by similarity), NM_001318057 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.482+6C>T
g.37620C>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	rs79375065
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	491	14037	14528

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.74	0
	0.452	0.118
(flanking)	4.84	0.998

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor weakened	37614	wt: 4.69 / mu: 8.34	-	wt: GGTTTCAACA\|gtgagcgctt mu: GGTTTCAACA\|gtgagtgctt

Distance from splice site

6

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

4

Strand

-1

Original gDNA sequence snippet

CCTTGGGTTTCAACAGTGAGCGCTTGTATCAGTGGATTTTC

Altered gDNA sequence snippet

CCTTGGGTTTCAACAGTGAGTGCTTGTATCAGTGGATTTTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MKLLHVFLLF LCFHLRFCKV TYTSQEDLVE KKCLAKKYTH LSCDKVFCQP WQRCIEGTCV
CKLPYQCPKN GTAVCATNRR SFPTYCQQKS LECLHPGTKF LNNGTCTAEG KFSVSLKHGN
TDSEGIVEVK LVDQDKTMFI CKSSWSMREA NVACLDLGFQ QGADTQRRFK LSDLSINSTE
CLHVHCRGLE TSLAECTFTK RRTMGYQDFA DVVCYTQKAD SPMDDFFQCV NGKYISQMKA
CDGINDCGDQ SDELCCKACQ GKGFHCKSGV CIPSQYQCNG EVDCITGEDE VGCAAARHPT
IQGFASVTQE ETEILTADMD AERRRIKSLL PKLSCGVKNR MHIRRKRIVG GKRAQLGDLP
WQVAIKDASG ITCGGIYIGG CWILTAAHCL RASKTHRYQI WTTVVDWIHP DLKRIVIEYV
DRIIFHENYN AGTYQNDIAL IEMKKDGNKK DCELPRSIPA CVPWSPYLFQ PNDTCIVSGW
GREKDNERVF SLQWGEVKLI SNCSKFYGNR FYEKEMECAG TYDGSIDACK GDSGGPLVCM
DANNVTYVWG VVSWGENCGK PEFPGVYTKV ANYFDWISYH VGRPFISQYN V*

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

29 / 29

Last intron/exon boundary

1586

Theoretical NMD boundary in CDS

1507

Length of CDS

1776

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

37620

Chromosomal position

109764531

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:

4:109764531G>A_4_ENST00000512148

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Splice site changes

Model: without_aae
Tree vote: 171|29 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr4:109764531G>A (GRCh38)

Gene symbol

CFI

Gene constraints

LOEUF: 1.08, LOF (oe): 0.85, misssense (oe): 0.97, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000512148.5

Genbank transcript ID

NM_001375282 (by similarity), NM_001375280 (by similarity), NM_001375283 (by similarity), NM_001331035 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.482+6C>T
g.37620C>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	rs79375065
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	491	14037	14528

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.74	0
	0.452	0.118
(flanking)	4.84	0.998

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor weakened	37614	wt: 4.69 / mu: 8.34	-	wt: GGTTTCAACA\|gtgagcgctt mu: GGTTTCAACA\|gtgagtgctt

Distance from splice site

6

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

4

Strand

-1

Original gDNA sequence snippet

CCTTGGGTTTCAACAGTGAGCGCTTGTATCAGTGGATTTTC

Altered gDNA sequence snippet

CCTTGGGTTTCAACAGTGAGTGCTTGTATCAGTGGATTTTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MKLLHVFLLF LCFHLRFCKV TYTSQEDLVE KKCLAKKYTH LSCDKVFCQP WQRCIEGTCV
CKLPYQCPKN GTAVCATNRR SFPTYCQQKS LECLHPGTKF LNNGTCTAEG KFSVSLKHGN
TDSEGIVEVK LVDQDKTMFI CKSSWSMREA NVACLDLGFQ QGADTQRRFK LSDLSINSTE
CLHVHCRGLE TSLAECTFTK RRTMGYQDFA DVVCYTQKAD SPMDDFFQCV NGKYISQMKA
CDGINDCGDQ SDELCCKACQ GKGFHCKSGV CIPSQYQCNG EVDCITGEDE VGCAEETEIL
TADMDAERRR IKSLLPKLSC GVKNRMHIRR KRIVGGKRAQ LGDLPWQVAI KDASGITCGG
IYIGGCWILT AAHCLRASKT HRYQIWTTVV DWIHPDLKRI VIEYVDRIIF HENYNAGTYQ
NDIALIEMKK DGNKKDCELP RSIPACVPWS PYLFQPNDTC IVSGWGREKD NERVFSLQWG
EVKLISNCSK FYGNRFYEKE MECAGTYDGS IDACKGDSGG PLVCMDANNV TYVWGVVSWG
ENCGKPEFPG VYTKVANYFD WISYHVGRPF ISQYNV*

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

15 / 15

Last intron/exon boundary

1527

Theoretical NMD boundary in CDS

1462

Length of CDS

1731

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

37620

Chromosomal position

109764531

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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Problem:

1

MutationT@ster 2025

Data problem

No NCBI gene ID found.

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