rs7595886

chr2-191174012-C-T

Variant summary

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

The XM_047445600.1(STAT4):c.-1403G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,106 control chromosomes in the GnomAD database, including 7,348 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 0.25 (7348 hom., cov: 32)
• Consequence: STAT4 XM_047445600.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

STAT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4	XM_047445600.1	c.-1403G>A		5_prime_UTR_variant	4/27
STAT4	XM_047445601.1	c.-1403G>A		5_prime_UTR_variant	4/27
STAT4	XM_047445602.1	c.-204G>A		5_prime_UTR_variant	6/30

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37491 AN: 151988 Hom.: 7319 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.247 AC: 37577 AN: 152106 Hom.: 7348 Cov.: 32 AF XY: 0.239 AC XY: 17793 AN XY: 74358

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0643

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.233

Alfa AF: 0.148 Hom.: 3706

Bravo AF: 0.268

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.63
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7595886; hg19: chr2-192038738;