2-191090126-G-A

Position:

• chr2-191090126-G-A

Variant summary

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

The NM_003151.4(STAT4):​c.274-13801C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 151,958 control chromosomes in the GnomAD database, including 33,400 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 0.66 (33400 hom., cov: 31)
• Consequence: STAT4 NM_003151.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAT4	NM_003151.4	c.274-13801C>T		intron_variant		ENST00000392320.7	NP_003142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAT4	ENST00000392320.7	c.274-13801C>T		intron_variant		1	NM_003151.4	ENSP00000376134	P1

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100342 AN: 151842 Hom.: 33387 Cov.: 31

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.661 AC: 100389 AN: 151958 Hom.: 33400 Cov.: 31 AF XY: 0.660 AC XY: 48986 AN XY: 74276

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.662

Alfa AF: 0.676 Hom.: 69324

Bravo AF: 0.649

Asia WGS AF: 0.565 AC: 1962 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.87
DANN	Benign	0.37

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: rs10931481; hg19: chr2-191954852;