rs11079041

Positions:

• chr17-42262061-T-A
• chr17-42262061-T-C
• chr17-42262061-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012448.4(STAT5B):​c.-11+14187A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,062 control chromosomes in the GnomAD database, including 11,120 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 0.36 (11120 hom., cov: 32)
• Consequence: STAT5B NM_012448.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT5B	NM_012448.4	c.-11+14187A>T		intron_variant		ENST00000293328.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAT5B	ENST00000293328.8	c.-11+14187A>T		intron_variant		1	NM_012448.4	P4

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54700 AN: 151944 Hom.: 11102 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.359

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.360 AC: 54769 AN: 152062 Hom.: 11120 Cov.: 32 AF XY: 0.357 AC XY: 26507 AN XY: 74320

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.359

Alfa AF: 0.189 Hom.: 405

Bravo AF: 0.363

Asia WGS AF: 0.435 AC: 1510 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.82
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11079041; hg19: chr17-40414079;