chr17-42201524-GCACACACACACACACACACA-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_012448.4(STAT5B):c.*194_*213delTGTGTGTGTGTGTGTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 617,404 control chromosomes in the GnomAD database, including 10 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0032 ( 4 hom., cov: 21)
Exomes 𝑓: 0.00045 ( 6 hom. )
Consequence
STAT5B
NM_012448.4 3_prime_UTR
NM_012448.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.22
Genes affected
STAT5B (HGNC:11367): (signal transducer and activator of transcription 5B) 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 mediates the signal transduction triggered by various cell ligands, such as IL2, IL4, CSF1, and different growth hormones. It has been shown to be involved in diverse biological processes, such as TCR signaling, apoptosis, adult mammary gland development, and sexual dimorphism of liver gene expression. This gene was found to fuse to retinoic acid receptor-alpha (RARA) gene in a small subset of acute promyelocytic leukemias (APLL). The dysregulation of the signaling pathways mediated by this protein may be the cause of the APLL. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00324 (473/145828) while in subpopulation AFR AF= 0.0114 (459/40248). AF 95% confidence interval is 0.0105. There are 4 homozygotes in gnomad4. There are 216 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 4 SD gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00325 AC: 473AN: 145738Hom.: 4 Cov.: 21
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GnomAD4 exome AF: 0.000450 AC: 212AN: 471576Hom.: 6 AF XY: 0.000386 AC XY: 96AN XY: 248628
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GnomAD4 genome AF: 0.00324 AC: 473AN: 145828Hom.: 4 Cov.: 21 AF XY: 0.00305 AC XY: 216AN XY: 70840
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at