12-57096045-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003153.5(STAT6):c.*527G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 154,210 control chromosomes in the GnomAD database, including 13,408 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 0.39 ( 13218 hom., cov: 32)
Exomes 𝑓: 0.41 ( 190 hom. )
Consequence
STAT6
NM_003153.5 3_prime_UTR
NM_003153.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.40
Publications
39 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=-0.79).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.389 AC: 59164AN: 151930Hom.: 13216 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
59164
AN:
151930
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:
GnomAD4 exome AF: 0.415 AC: 897AN: 2162Hom.: 190 Cov.: 0 AF XY: 0.424 AC XY: 486AN XY: 1146 show subpopulations
GnomAD4 exome
AF:
AC:
897
AN:
2162
Hom.:
Cov.:
0
AF XY:
AC XY:
486
AN XY:
1146
show subpopulations
African (AFR)
AF:
AC:
14
AN:
84
American (AMR)
AF:
AC:
20
AN:
56
Ashkenazi Jewish (ASJ)
AF:
AC:
20
AN:
56
East Asian (EAS)
AF:
AC:
17
AN:
114
South Asian (SAS)
AF:
AC:
14
AN:
36
European-Finnish (FIN)
AF:
AC:
60
AN:
124
Middle Eastern (MID)
AF:
AC:
5
AN:
16
European-Non Finnish (NFE)
AF:
AC:
689
AN:
1548
Other (OTH)
AF:
AC:
58
AN:
128
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.487
Heterozygous variant carriers
0
28
56
85
113
141
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.389 AC: 59165AN: 152048Hom.: 13218 Cov.: 32 AF XY: 0.388 AC XY: 28803AN XY: 74302 show subpopulations
GnomAD4 genome
AF:
AC:
59165
AN:
152048
Hom.:
Cov.:
32
AF XY:
AC XY:
28803
AN XY:
74302
show subpopulations
African (AFR)
AF:
AC:
6891
AN:
41476
American (AMR)
AF:
AC:
6646
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
1548
AN:
3466
East Asian (EAS)
AF:
AC:
1305
AN:
5154
South Asian (SAS)
AF:
AC:
2043
AN:
4820
European-Finnish (FIN)
AF:
AC:
5279
AN:
10580
Middle Eastern (MID)
AF:
AC:
121
AN:
292
European-Non Finnish (NFE)
AF:
AC:
34224
AN:
67960
Other (OTH)
AF:
AC:
841
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1711
3422
5132
6843
8554
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1153
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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