chr12-57102832-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_003153.5(STAT6):c.1302G>A(p.Glu434=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,613,514 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000062 ( 0 hom. )
Consequence
STAT6
NM_003153.5 synonymous
NM_003153.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.163
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 made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
?
Variant 12-57102832-C-T is Benign according to our data. Variant chr12-57102832-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2643110.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.163 with no splicing effect.
BS2
?
High AC in GnomAd at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAT6 | NM_003153.5 | c.1302G>A | p.Glu434= | synonymous_variant | 12/22 | ENST00000300134.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAT6 | ENST00000300134.8 | c.1302G>A | p.Glu434= | synonymous_variant | 12/22 | 1 | NM_003153.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152058Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251360Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135846
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GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461456Hom.: 0 Cov.: 32 AF XY: 0.0000729 AC XY: 53AN XY: 727082
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GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152058Hom.: 0 Cov.: 30 AF XY: 0.0000808 AC XY: 6AN XY: 74280
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | STAT6: BP4, BP7 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at