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: ENST00000549336
Querying Taster for transcript #2: ENST00000395324
Querying Taster for transcript #3: ENST00000550325
Querying Taster for transcript #4: ENST00000229022
MT speed 0.08 s - this script 2.456855 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
ENST00000549336(MANE Select)	VDR	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000395324	VDR	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000550325	VDR	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000229022	VDR	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

12:47845054C>A_1_ENST00000549336

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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

Chr12:47845054C>A (GRCh38)

Gene symbol

VDR

Gene constraints

LOEUF: 0.71, LOF (oe): 0.49, misssense (oe): 0.75, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000549336.6

Genbank transcript ID

NM_000376 (exact from MANE), NM_001374662 (by similarity), NM_001017535 (by similarity), NM_001374661 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1025-49G>T
g.97995G>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	rs7975232
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-1.016	0
	-0.874	0
(flanking)	-0.008	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

12

Strand

-1

Original gDNA sequence snippet

GGTGGGATTGAGCAGTGAGGGGCCCAGCTGAGAGCTCCTGT

Altered gDNA sequence snippet

GGTGGGATTGAGCAGTGAGGTGCCCAGCTGAGAGCTCCTGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEAMAASTSL PDPGDFDRNV PRICGVCGDR ATGFHFNAMT CEGCKGFFRR SMKRKALFTC
PFNGDCRITK DNRRHCQACR LKRCVDIGMM KEFILTDEEV QRKREMILKR KEEEALKDSL
RPKLSEEQQR IIAILLDAHH KTYDPTYSDF CQFRPPVRVN DGGGSHPSRP NSRHTPSFSG
DSSSSCSDHC ITSSDMMDSS SFSNLDLSEE DSDDPSVTLE LSQLSMLPHL ADLVSYSIQK
VIGFAKMIPG FRDLTSEDQI VLLKSSAIEV IMLRSNESFT MDDMSWTCGN QDYKYRVSDV
TKAGHSLELI EPLIKFQVGL KKLNLHEEEH VLLMAICIVS PDRPGVQDAA LIEAIQDRLS
NTLQTYIRCR HPPPGSHLLY AKMIQKLADL RSLNEEHSKQ YRCLSFQPEC SMKLTPLVLE
VFGNEIS*

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

124 / 124

Last intron/exon boundary

1147

Theoretical NMD boundary in CDS

973

Length of CDS

1284

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

97995

Chromosomal position

47845054

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:

12:47845054C>A_2_ENST00000395324

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

Chr12:47845054C>A (GRCh38)

Gene symbol

VDR

Gene constraints

LOEUF: 0.71, LOF (oe): 0.49, misssense (oe): 0.75, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000395324.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1025-49G>T
g.97995G>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	rs7975232
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-1.016	0
	-0.874	0
(flanking)	-0.008	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

12

Strand

-1

Original gDNA sequence snippet

GGTGGGATTGAGCAGTGAGGGGCCCAGCTGAGAGCTCCTGT

Altered gDNA sequence snippet

GGTGGGATTGAGCAGTGAGGTGCCCAGCTGAGAGCTCCTGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEAMAASTSL PDPGDFDRNV PRICGVCGDR ATGFHFNAMT CEGCKGFFRR SMKRKALFTC
PFNGDCRITK DNRRHCQACR LKRCVDIGMM KEFILTDEEV QRKREMILKR KEEEALKDSL
RPKLSEEQQR IIAILLDAHH KTYDPTYSDF CQFRPPVRVN DGGGSHPSRP NSRHTPSFSG
DSSSSCSDHC ITSSDMMDSS SFSNLDLSEE DSDDPSVTLE LSQLSMLPHL ADLVSYSIQK
VIGFAKMIPG FRDLTSEDQI VLLKSSAIEV IMLRSNESFT MDDMSWTCGN QDYKYRVSDV
TKAGHSLELI EPLIKFQVGL KKLNLHEEEH VLLMAICIVS PDRPGVQDAA LIEAIQDRLS
NTLQTYIRCR HPPPGSHLLY AKMIQKLADL RSLNEEHSKQ YRCLSFQPEC SMKLTPLVLE
VFGNEIS*

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

270 / 270

Last intron/exon boundary

1293

Theoretical NMD boundary in CDS

973

Length of CDS

1284

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

97995

Chromosomal position

47845054

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:

12:47845054C>A_3_ENST00000550325

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

Chr12:47845054C>A (GRCh38)

Gene symbol

VDR

Gene constraints

LOEUF: 0.78, LOF (oe): 0.57, misssense (oe): 0.80, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000550325.5

Genbank transcript ID

NM_001017536 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1175-49G>T
g.97995G>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	rs7975232
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-1.016	0
	-0.874	0
(flanking)	-0.008	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

12

Strand

-1

Original gDNA sequence snippet

GGTGGGATTGAGCAGTGAGGGGCCCAGCTGAGAGCTCCTGT

Altered gDNA sequence snippet

GGTGGGATTGAGCAGTGAGGTGCCCAGCTGAGAGCTCCTGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEWRNKKRSD WLSMVLRTAG VEEAFGSEVS VRPHRRAPLG STYLPPAPSG MEAMAASTSL
PDPGDFDRNV PRICGVCGDR ATGFHFNAMT CEGCKGFFRR SMKRKALFTC PFNGDCRITK
DNRRHCQACR LKRCVDIGMM KEFILTDEEV QRKREMILKR KEEEALKDSL RPKLSEEQQR
IIAILLDAHH KTYDPTYSDF CQFRPPVRVN DGGGSHPSRP NSRHTPSFSG DSSSSCSDHC
ITSSDMMDSS SFSNLDLSEE DSDDPSVTLE LSQLSMLPHL ADLVSYSIQK VIGFAKMIPG
FRDLTSEDQI VLLKSSAIEV IMLRSNESFT MDDMSWTCGN QDYKYRVSDV TKAGHSLELI
EPLIKFQVGL KKLNLHEEEH VLLMAICIVS PDRPGVQDAA LIEAIQDRLS NTLQTYIRCR
HPPPGSHLLY AKMIQKLADL RSLNEEHSKQ YRCLSFQPEC SMKLTPLVLE VFGNEIS*

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

374 / 374

Last intron/exon boundary

1547

Theoretical NMD boundary in CDS

1123

Length of CDS

1434

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

97995

Chromosomal position

47845054

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:

12:47845054C>A_4_ENST00000229022

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

Chr12:47845054C>A (GRCh38)

Gene symbol

VDR

Gene constraints

LOEUF: 0.78, LOF (oe): 0.53, misssense (oe): 0.77, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000229022.9

Genbank transcript ID

NM_001364085 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1025-49G>T
g.97995G>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	rs7975232
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-1.016	0
	-0.874	0
(flanking)	-0.008	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

12

Strand

-1

Original gDNA sequence snippet

GGTGGGATTGAGCAGTGAGGGGCCCAGCTGAGAGCTCCTGT

Altered gDNA sequence snippet

GGTGGGATTGAGCAGTGAGGTGCCCAGCTGAGAGCTCCTGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEAMAASTSL PDPGDFDRNV PRICGVCGDR ATGFHFNAMT CEGCKGFFRR SMKRKALFTC
PFNGDCRITK DNRRHCQACR LKRCVDIGMM KEFILTDEEV QRKREMILKR KEEEALKDSL
RPKLSEEQQR IIAILLDAHH KTYDPTYSDF CQFRPPVRVN DGGGSHPSRP NSRHTPSFSG
DSSSSCSDHC ITSSDMMDSS SFSNLDLSEE DSDDPSVTLE LSQLSMLPHL ADLVSYSIQK
VIGFAKMIPG FRDLTSEDQI VLLKSSAIEV IMLRSNESFT MDDMSWTCGN QDYKYRVSDV
TKAGHSLELI EPLIKFQVGL KKLNLHEEEH VLLMAICIVS PDRPGVQDAA LIEAIQDRLS
NTLQTYIRCR HPPPGSHLLY AKMIQKLADL RSLNEEHSKQ YRCLSFQPEC SMKLTPLVLE
VFGNEIS*

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

3 / 3

Last intron/exon boundary

1026

Theoretical NMD boundary in CDS

973

Length of CDS

1485

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

97995

Chromosomal position

47845054

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