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: ENST00000221700
Querying Taster for transcript #2: ENST00000011989
MT speed 0.04 s - this script 2.421577 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000221700(MANE Select)	CYP4F2	Benign	0\|200	without_aae		No				Single base exchange		N/A	Homozygous in gnomAD
ENST00000011989	CYP4F2	Benign	0\|200	without_aae		No				Single base exchange		N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

19:15897659C>G_1_ENST00000221700

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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

Chr19:15897659C>G (GRCh38)

Gene symbol

CYP4F2

Gene constraints

LOEUF: 1.20, LOF (oe): 0.96, misssense (oe): 0.89, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000221700.11

Genbank transcript ID

NM_001082 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-1-47G>C
g.419G>C

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	rs3093100
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	22810	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.34	0
	-1.261	0
(flanking)	-3.258	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

19

Strand

-1

Original gDNA sequence snippet

TCCCTGGAGGTCCCTGGGCCGTTCTCTGGGCCTCAGGATCT

Altered gDNA sequence snippet

TCCCTGGAGGTCCCTGGGCCCTTCTCTGGGCCTCAGGATCT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSQLSLSWLG LWPVAASPWL LLLLVGASWL LAHVLAWTYA FYDNCRRLRC FPQPPRRNWF
WGHQGMVNPT EEGMRVLTQL VATYPQGFKV WMGPISPLLS LCHPDIIRSV INASAAIAPK
DKFFYSFLEP WLGDGLLLSA GDKWSRHRRM LTPAFHFNIL KPYMKIFNES VNIMHAKWQL
LASEGSACLD MFEHISLMTL DSLQKCVFSF DSHCQEKPSE YIAAILELSA LVSKRHHEIL
LHIDFLYYLT PDGQRFRRAC RLVHDFTDAV IQERRRTLPS QGVDDFLQAK AKSKTLDFID
VLLLSKDEDG KKLSDEDIRA EADTFMFEGH DTTASGLSWV LYHLAKHPEY QERCRQEVQE
LLKDREPKEI EWDDLAHLPF LTMCMKESLR LHPPVPVISR HVTQDIVLPD GRVIPKGIIC
LISVFGTHHN PAVWPDPEVY DPFRFDPENI KERSPLAFIP FSAGPRNCIG QTFAMAEMKV
VLALTLLRFR VLPDHTEPRR KPELVLRAEG GLWLRVEPLS *

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

51 / 51

Last intron/exon boundary

1447

Theoretical NMD boundary in CDS

1346

Length of CDS

1563

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

419

Chromosomal position

15897659

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:

19:15897659C>G_2_ENST00000011989

Back to summary table

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

Chr19:15897659C>G (GRCh38)

Gene symbol

CYP4F2

Gene constraints

LOEUF: 1.21, LOF (oe): 0.96, misssense (oe): 0.88, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000011989.11

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-1-47G>C
g.419G>C

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	rs3093100
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	22810	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.34	0
	-1.261	0
(flanking)	-3.258	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

19

Strand

-1

Original gDNA sequence snippet

TCCCTGGAGGTCCCTGGGCCGTTCTCTGGGCCTCAGGATCT

Altered gDNA sequence snippet

TCCCTGGAGGTCCCTGGGCCCTTCTCTGGGCCTCAGGATCT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSQLSLSWLG LWPVAASPWL LLLLVGASWL LAHVLAWTYA FYDNCRRLRC FPQPPRRNWF
WGHQGMIHSS EEGLLYTQSL ACTFGDMGCW WVGPWQAVIH IFLPTCIKPV LFAPAAIAPK
DKFFYSFLEP WLGDGLLLSA GDKWSRHRRM LTPAFHFNIL KPYMKIFNES VNIMHAKWQL
LASEGSACLD MFEHISLMTL DSLQKCVFSF DSHCQEKPSE YIAAILELSA LVSKRHHEIL
LHIDFLYYLT PDGQRFRRAC RLVHDFTDAV IQERRRTLPS QGVDDFLQAK AKSKTLDFID
VLLLSKDEDG KKLSDEDIRA EADTFMFEGH DTTASGLSWV LYHLAKHPEY QERCRQEVQE
LLKDREPKEI EWDDLAHLPF LTMCMKESLR LHPPVPVISR HVTQDIVLPD GRVIPKGIIC
LISVFGTHHN PAVWPDPEVY DPFRFDPENI KERSPLAFIP FSAGPRNCIG QTFAMAEMKV
VLALTLLRFR VLPDHTEPRR KPELVLRAEG GLWLRVEPLS *

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

34 / 34

Last intron/exon boundary

1430

Theoretical NMD boundary in CDS

1346

Length of CDS

1563

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

419

Chromosomal position

15897659

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