rs2272087
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001288718.2(STAT5A):c.1775+48A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,613,682 control chromosomes in the GnomAD database, including 30,926 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 0.21 ( 3533 hom., cov: 32)
Exomes 𝑓: 0.19 ( 27393 hom. )
Consequence
STAT5A
NM_001288718.2 intron
NM_001288718.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.246
Genes affected
STAT5A (HGNC:11366): (signal transducer and activator of transcription 5A) 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 activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2013]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAT5A | NM_001288718.2 | c.1775+48A>G | intron_variant | ENST00000590949.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAT5A | ENST00000590949.6 | c.1775+48A>G | intron_variant | 1 | NM_001288718.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.205 AC: 31178AN: 151808Hom.: 3525 Cov.: 32
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GnomAD3 exomes AF: 0.197 AC: 49390AN: 251040Hom.: 5582 AF XY: 0.203 AC XY: 27507AN XY: 135710
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GnomAD4 exome AF: 0.186 AC: 272108AN: 1461756Hom.: 27393 Cov.: 35 AF XY: 0.190 AC XY: 138194AN XY: 727164
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GnomAD4 genome ? AF: 0.206 AC: 31225AN: 151926Hom.: 3533 Cov.: 32 AF XY: 0.207 AC XY: 15410AN XY: 74274
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at