rs3024861

Positions:

• chr2-191059880-T-A

Variant summary

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

The NM_003151.4(STAT4):​c.1035-1111A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,994 control chromosomes in the GnomAD database, including 28,622 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 0.57 (28622 hom., cov: 31)
• Consequence: STAT4 NM_003151.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4	NM_003151.4	c.1035-1111A>T		intron_variant		ENST00000392320.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAT4	ENST00000392320.7	c.1035-1111A>T		intron_variant		1	NM_003151.4	P1
STAT4	ENST00000358470.8	c.1035-1111A>T		intron_variant		1		P1
	ENST00000658263.1	n.1301-4904T>A		intron_variant, non_coding_transcript_variant
STAT4	ENST00000495849.5	n.1103-1111A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86472 AN: 151876 Hom.: 28627 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.569 AC: 86470 AN: 151994 Hom.: 28622 Cov.: 31 AF XY: 0.569 AC XY: 42260 AN XY: 74298

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.600

Alfa AF: 0.653 Hom.: 4398

Bravo AF: 0.541

Asia WGS AF: 0.560 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.51

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: rs3024861; hg19: chr2-191924606;