rs3024971
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003153.5(STAT6):c.1608-41A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0941 in 1,613,844 control chromosomes in the GnomAD database, including 7,802 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 0.079 ( 565 hom., cov: 32)
Exomes 𝑓: 0.096 ( 7237 hom. )
Consequence
STAT6
NM_003153.5 intron
NM_003153.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.773
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAT6 | NM_003153.5 | c.1608-41A>C | intron_variant | ENST00000300134.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAT6 | ENST00000300134.8 | c.1608-41A>C | intron_variant | 1 | NM_003153.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0793 AC: 12051AN: 151906Hom.: 564 Cov.: 32
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GnomAD3 exomes AF: 0.0775 AC: 19472AN: 251160Hom.: 863 AF XY: 0.0790 AC XY: 10721AN XY: 135740
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GnomAD4 exome AF: 0.0956 AC: 139818AN: 1461818Hom.: 7237 Cov.: 33 AF XY: 0.0946 AC XY: 68767AN XY: 727206
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GnomAD4 genome ? AF: 0.0793 AC: 12053AN: 152026Hom.: 565 Cov.: 32 AF XY: 0.0772 AC XY: 5736AN XY: 74326
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at