rs3024980

chr12-57104697-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_003153.5(STAT6):c.1089+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0116 in 1,613,920 control chromosomes in the GnomAD database, including 149 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 0.0082 (9 hom., cov: 32)
  • Exomes 𝑓: 0.012 (140 hom.)
• Consequence: STAT6 NM_003153.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS2: High AC in GnomAd at 1247 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT6	NM_003153.5	c.1089+29G>A		intron_variant		ENST00000300134.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAT6	ENST00000300134.8	c.1089+29G>A		intron_variant		1	NM_003153.5	P1

Frequencies

GnomAD3 genomes AF: 0.00820 AC: 1247 AN: 152130 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.00234

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.00222

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.00335

GnomAD3 exomes AF: 0.00890 AC: 2235 AN: 251044 Hom.: 17 AF XY: 0.00899 AC XY: 1220 AN XY: 135652

Gnomad AFR exome AF: 0.00234

Gnomad AMR exome AF: 0.00220

Gnomad ASJ exome AF: 0.000199

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00111

Gnomad FIN exome AF: 0.0188

Gnomad NFE exome AF: 0.0141

Gnomad OTH exome AF: 0.0123

GnomAD4 exome AF: 0.0119 AC: 17420 AN: 1461672 Hom.: 140 Cov.: 31 AF XY: 0.0115 AC XY: 8368 AN XY: 727126

Gnomad4 AFR exome AF: 0.00212

Gnomad4 AMR exome AF: 0.00255

Gnomad4 ASJ exome AF: 0.000230

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00104

Gnomad4 FIN exome AF: 0.0189

Gnomad4 NFE exome AF: 0.0141

Gnomad4 OTH exome AF: 0.00782

GnomAD4 genome AF: 0.00819 AC: 1247 AN: 152248 Hom.: 9 Cov.: 32 AF XY: 0.00854 AC XY: 636 AN XY: 74442

Gnomad4 AFR AF: 0.00234

Gnomad4 AMR AF: 0.00222

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.0197

Gnomad4 NFE AF: 0.0130

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00775 Hom.: 2

Bravo AF: 0.00679

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.29
Dann	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3024980; hg19: chr12-57498480;