NM_003151.4:c.274-2691G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 classification points (ACMG Germline Pathogenicity v2019): 0P and 12B. BA1BP4_Strong
The NM_003151.4(STAT4):c.274-2691G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.212 (AC=32,161) in the gnomAD database across 151,872 control chromosomes, including 3,737 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.332. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.21 ( 3737 hom., cov: 31)
Consequence
STAT4
NM_003151.4 intron
NM_003151.4 intron
Scores
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.483
Publications
135 publications found
Genes affected
STAT4 (HGNC:11365): (signal transducer and activator of transcription 4) 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 is essential for mediating responses to IL12 in lymphocytes, and regulating the differentiation of T helper cells. Mutations in this gene may be associated with systemic lupus erythematosus and rheumatoid arthritis. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Aug 2011]
STAT4 Gene-Disease associations (from GenCC):
- disabling pansclerotic morphea of childhoodInheritance: AD Classification: STRONG, LIMITED Submitted by: PanelApp Australia, Ambry Genetics
- systemic lupus erythematosusInheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet
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new If you want to explore the variant's impact on the transcript NM_003151.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
Classification according to ACMG Germline Pathogenicity v2019
Classification was made for transcript
Our verdict: Benign. The variant received -12 points.
BP4
Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); Splicing verdict: benign (Strong).; Germline computational verdict: benign (Strong).
BA1
GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.3317 — exceeds 5%% threshold (BA1 applied)
Variant Effect in Transcripts
Automated classification analysis was done for transcript: NM_003151.4. You can select a different transcript below to see updated classification assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| STAT4 | TSL:1 MANE Select | c.274-2691G>A | intron | N/A | ENSP00000376134.2 | Q14765 | |||
| STAT4 | TSL:1 | c.274-2691G>A | intron | N/A | ENSP00000351255.4 | Q14765 | |||
| STAT4 | TSL:1 | c.274-2691G>A | intron | N/A | ENSP00000412397.2 | Q14765 |
Frequencies
GnomAD3 genomes 0.212 AC: 32136AN: 151756Hom.: 3728 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
32136
AN:
151756
Hom.:
Cov.:
31
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 0.212 AC: 32161AN: 151872Hom.: 3737 Cov.: 31 AF XY: 0.215 AC XY: 15967AN XY: 74216 show subpopulations
GnomAD4 genome
AF:
AC:
32161
AN:
151872
Hom.:
Cov.:
31
AF XY:
AC XY:
15967
AN XY:
74216
show subpopulations
African (AFR)
AF:
AC:
5387
AN:
41490
American (AMR)
AF:
AC:
4749
AN:
15246
Ashkenazi Jewish (ASJ)
AF:
AC:
800
AN:
3462
East Asian (EAS)
AF:
AC:
1781
AN:
5162
South Asian (SAS)
AF:
AC:
1185
AN:
4810
European-Finnish (FIN)
AF:
AC:
2426
AN:
10512
Middle Eastern (MID)
AF:
AC:
82
AN:
294
European-Non Finnish (NFE)
AF:
AC:
15100
AN:
67876
Other (OTH)
AF:
AC:
477
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1262
2524
3785
5047
6309
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
354
708
1062
1416
1770
<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:
1066
AN:
3478
Local populations
ToMMo 61KJPN (+60KJPN MNV)
AF:
AC:
37842
AN:
121816
Turkish Variome
AF:
AC:
398
AN:
1546
Hom.:
WBBC (Westlake BioBank for Chinese) pilot
AF:
AC:
3045
AN:
8960
Hom.:
ABraOM SABE-WGS-1171
AF:
AC:
536
AN:
2342
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
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Other links and lift over
dbSNP: rs11889341 ;
hg19: chr2-191943742;