rs57081321

Positions:

• chr2-191160259-T-C

Variant summary

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

The XM_047445600.1(STAT4):​c.27-12055A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,090 control chromosomes in the GnomAD database, including 24,931 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 0.56 (24931 hom., cov: 33)
• Consequence: STAT4 XM_047445600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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 = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4	XM_047445600.1	c.27-12055A>G		intron_variant
STAT4	XM_047445601.1	c.27-12055A>G		intron_variant
STAT4	XM_047445602.1	c.27-12055A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84431 AN: 151972 Hom.: 24916 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.556 AC: 84492 AN: 152090 Hom.: 24931 Cov.: 33 AF XY: 0.562 AC XY: 41775 AN XY: 74318

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.548

Alfa AF: 0.609 Hom.: 3702

Bravo AF: 0.544

Asia WGS AF: 0.542 AC: 1881 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	0.47
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57081321; hg19: chr2-192024985;