2-191160178-A-G

Variant summary

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

The XM_047445600.1(STAT4):c.27-11974T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,072 control chromosomes in the GnomAD database, including 31,301 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 0.63 (31301 hom., cov: 33)
• Consequence: STAT4 XM_047445600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

Genes affected

STAT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4	XM_047445600.1	c.27-11974T>C		intron_variant
STAT4	XM_047445601.1	c.27-11974T>C		intron_variant
STAT4	XM_047445602.1	c.27-11974T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95749 AN: 151954 Hom.: 31285 Cov.: 33

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.630 AC: 95816 AN: 152072 Hom.: 31301 Cov.: 33 AF XY: 0.635 AC XY: 47181 AN XY: 74316

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.623

Alfa AF: 0.693 Hom.: 60195

Bravo AF: 0.620

Asia WGS AF: 0.645 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	4.0
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13001658; hg19: chr2-192024904;