1-220880008-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_021958.4(HLX):c.151C>T(p.His51Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000139 in 1,443,754 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
HLX
NM_021958.4 missense
NM_021958.4 missense
Scores
4
10
4
Clinical Significance
Conservation
PhyloP100: 5.37
Publications
0 publications found
Genes affected
HLX (HGNC:4978): (H2.0 like homeobox) Enables sequence-specific DNA binding activity. Predicted to be involved in cell differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including animal organ development; enteric nervous system development; and regulation of T-helper cell differentiation. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]
ENSG00000286231 (HGNC:):
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_021958.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| HLX | TSL:1 MANE Select | c.151C>T | p.His51Tyr | missense | Exon 1 of 4 | ENSP00000355870.5 | Q14774 | ||
| ENSG00000286231 | n.843-1186C>T | intron | N/A | ENSP00000499157.1 | A0A494C1P3 | ||||
| HLX | c.151C>T | p.His51Tyr | missense | Exon 1 of 4 | ENSP00000614573.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1443754Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 718220 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1443754
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
718220
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33300
American (AMR)
AF:
AC:
0
AN:
44244
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25960
East Asian (EAS)
AF:
AC:
2
AN:
39564
South Asian (SAS)
AF:
AC:
0
AN:
85656
European-Finnish (FIN)
AF:
AC:
0
AN:
40030
Middle Eastern (MID)
AF:
AC:
0
AN:
5388
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1109650
Other (OTH)
AF:
AC:
0
AN:
59962
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
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
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
D
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Pathogenic
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of phosphorylation at H51 (P = 0.0502)
MVP
MPC
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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