10-101131680-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_005521.4(TLX1):c.139C>A(p.Leu47Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TLX1
NM_005521.4 missense
NM_005521.4 missense
Scores
2
5
11
Clinical Significance
Conservation
PhyloP100: 0.808
Publications
0 publications found
Genes affected
TLX1 (HGNC:5056): (T cell leukemia homeobox 1) This gene encodes a nuclear transcription factor that belongs to the NK-linked or NK-like (NKL) subfamily of homeobox genes. The encoded protein is required for normal development of the spleen during embryogenesis. This protein is also involved in specification of neuronal cell fates. Ectopic expression of this gene due to chromosomal translocations is associated with certain T-cell acute lymphoblastic leukemias. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3534878).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005521.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TLX1 | TSL:1 MANE Select | c.139C>A | p.Leu47Ile | missense | Exon 1 of 3 | ENSP00000359215.6 | P31314-1 | ||
| TLX1 | TSL:1 | c.139C>A | p.Leu47Ile | missense | Exon 1 of 3 | ENSP00000434914.2 | P31314-2 | ||
| TLX1NB | n.732-4582G>T | intron | N/A |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1388170Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 689208
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1388170
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
689208
African (AFR)
AF:
AC:
0
AN:
27940
American (AMR)
AF:
AC:
0
AN:
33008
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22726
East Asian (EAS)
AF:
AC:
0
AN:
33320
South Asian (SAS)
AF:
AC:
0
AN:
76116
European-Finnish (FIN)
AF:
AC:
0
AN:
50348
Middle Eastern (MID)
AF:
AC:
0
AN:
5486
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1082108
Other (OTH)
AF:
AC:
0
AN:
57118
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
P
Vest4
MutPred
Gain of sheet (P = 0.0827)
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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