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: ENST00000374429
Querying Taster for transcript #2: ENST00000395793
MT speed 0.17 s - this script 2.499671 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
ENST00000374429	CXCL12	Benign	0\|100	3utr		No				Single base exchange		N/A	Homozygous in gnomAD
ENST00000395793	CXCL12	Benign	0\|100	3utr		No				Single base exchange		N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

10:44372809C>T_1_ENST00000374429

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 3utr
Tree vote: 0|100 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr10:44372809C>T (GRCh38)

Gene symbol

CXCL12

Gene constraints

LOEUF: 1.21, LOF (oe): 0.64, misssense (oe): 1.18, synonymous (oe): 1.21 ? (gnomAD)

Ensembl transcript ID

ENST00000374429.6

Genbank transcript ID

NM_000609 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.888G>A
g.13685G>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	rs1801157
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	28295	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.293	0
	-0.813	0
(flanking)	-2.34	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

polyA signal ok

AA sequence altered

N/A

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TCTCCATCCACATGGGAGCCGGGTCTGCCTCTTCTGGGAGG

Altered gDNA sequence snippet

TCTCCATCCACATGGGAGCCAGGTCTGCCTCTTCTGGGAGG

Original cDNA sequence snippet

TCTCCATCCACATGGGAGCCGGGTCTGCCTCTTCTGGGAGG

Altered cDNA sequence snippet

TCTCCATCCACATGGGAGCCAGGTCTGCCTCTTCTGGGAGG

Wildtype AA sequence

MNAKVVVVLV LVLTALCLSD GKPVSLSYRC PCRFFESHVA RANVKHLKIL NTPNCALQIV
ARLKNNNRQV CIDPKLKWIQ EYLEKALNKR FKM*

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

88 / 88

Last intron/exon boundary

353

Theoretical NMD boundary in CDS

215

Length of CDS

282

Coding sequence (CDS) position

N/A

cDNA position

888

gDNA position

13685

Chromosomal position

44372809

Speed

0.09 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:

10:44372809C>T_2_ENST00000395793

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 3utr
Tree vote: 0|100 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr10:44372809C>T (GRCh38)

Gene symbol

CXCL12

Gene constraints

LOEUF: 1.76, LOF (oe): 0.80, misssense (oe): 1.01, synonymous (oe): 1.33 ? (gnomAD)

Ensembl transcript ID

ENST00000395793.7

Genbank transcript ID

NM_001277990 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.478G>A
g.13685G>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	rs1801157
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	28295	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.293	0
	-0.813	0
(flanking)	-2.34	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

polyA signal ok

AA sequence altered

N/A

Chromosome

10

Strand

-1

Original gDNA sequence snippet

TCTCCATCCACATGGGAGCCGGGTCTGCCTCTTCTGGGAGG

Altered gDNA sequence snippet

TCTCCATCCACATGGGAGCCAGGTCTGCCTCTTCTGGGAGG

Original cDNA sequence snippet

TCTCCATCCACATGGGAGCCGGGTCTGCCTCTTCTGGGAGG

Altered cDNA sequence snippet

TCTCCATCCACATGGGAGCCAGGTCTGCCTCTTCTGGGAGG

Wildtype AA sequence

MNAKVVVVLV LVLTALCLSD GKPVSLSYRC PCRFFESHYC TCLIRVSFHG ATPLTQGSWV
LYSLSCAGGE TGLREPGPMV SPRVESHQEG RLGVPGPVNL GKA*

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

88 / 88

Last intron/exon boundary

196

Theoretical NMD boundary in CDS

58

Length of CDS

312

Coding sequence (CDS) position

N/A

cDNA position

478

gDNA position

13685

Chromosomal position

44372809

Speed

0.08 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