rs3024921

Positions:

• chr2-191078546-A-T

Variant summary

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

The NM_003151.4(STAT4):​c.274-2221T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0358 in 152,258 control chromosomes in the GnomAD database, including 148 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 0.036 (148 hom., cov: 32)
• Consequence: STAT4 NM_003151.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.30

Genes affected

STAT4 (HGNC:11365): (signal transducer and activator of transcription 4) 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 essential for mediating responses to IL12 in lymphocytes, and regulating the differentiation of T helper cells. Mutations in this gene may be associated with systemic lupus erythematosus and rheumatoid arthritis. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4	NM_003151.4	c.274-2221T>A		intron_variant		ENST00000392320.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAT4	ENST00000392320.7	c.274-2221T>A		intron_variant		1	NM_003151.4	P1

Frequencies

GnomAD3 genomes AF: 0.0359 AC: 5457 AN: 152140 Hom.: 148 Cov.: 32

Gnomad AFR AF: 0.00984

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0191

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0277

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

GnomAD4 genome AF: 0.0358 AC: 5457 AN: 152258 Hom.: 148 Cov.: 32 AF XY: 0.0341 AC XY: 2537 AN XY: 74446

Gnomad4 AFR AF: 0.00982

Gnomad4 AMR AF: 0.0191

Gnomad4 ASJ AF: 0.0204

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0132

Gnomad4 FIN AF: 0.0271

Gnomad4 NFE AF: 0.0613

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.0538 Hom.: 38

Bravo AF: 0.0336

Asia WGS AF: 0.00982 AC: 34 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.55

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: rs3024921; hg19: chr2-191943272;