ENST00000556155.5:c.-21-4823G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000556155.5(STAT6):c.-21-4823G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 152,174 control chromosomes in the GnomAD database, including 584 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.075 ( 584 hom., cov: 32)
Consequence
STAT6
ENST00000556155.5 intron
ENST00000556155.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.381
Publications
11 publications found
Genes affected
STAT6 (HGNC:11368): (signal transducer and activator of transcription 6) The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein plays a central role in exerting IL4 mediated biological responses. It is found to induce the expression of BCL2L1/BCL-X(L), which is responsible for the anti-apoptotic activity of IL4. Knockout studies in mice suggested the roles of this gene in differentiation of T helper 2 (Th2) cells, expression of cell surface markers, and class switch of immunoglobulins. Alternative splicing results in multiple transcript variants.[provided by RefSeq, May 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC124902946 | XR_007063334.1 | n.*243C>T | downstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0749 AC: 11396AN: 152056Hom.: 584 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
11396
AN:
152056
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0748 AC: 11389AN: 152174Hom.: 584 Cov.: 32 AF XY: 0.0731 AC XY: 5439AN XY: 74392 show subpopulations
GnomAD4 genome
AF:
AC:
11389
AN:
152174
Hom.:
Cov.:
32
AF XY:
AC XY:
5439
AN XY:
74392
show subpopulations
African (AFR)
AF:
AC:
771
AN:
41508
American (AMR)
AF:
AC:
1153
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
483
AN:
3470
East Asian (EAS)
AF:
AC:
90
AN:
5174
South Asian (SAS)
AF:
AC:
448
AN:
4826
European-Finnish (FIN)
AF:
AC:
870
AN:
10610
Middle Eastern (MID)
AF:
AC:
48
AN:
294
European-Non Finnish (NFE)
AF:
AC:
7210
AN:
67988
Other (OTH)
AF:
AC:
214
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
521
1043
1564
2086
2607
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
134
268
402
536
670
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
157
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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