chr2-191158982-A-G

Position:

• chr2-191158982-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.27-10778T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,048 control chromosomes in the GnomAD database, including 24,330 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 0.54 (24330 hom., cov: 32)
• Consequence: STAT4 XM_047445600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

STAT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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.27-10778T>C		intron_variant
STAT4	XM_047445601.1	c.27-10778T>C		intron_variant
STAT4	XM_047445602.1	c.27-10778T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82773 AN: 151930 Hom.: 24321 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.545 AC: 82813 AN: 152048 Hom.: 24330 Cov.: 32 AF XY: 0.551 AC XY: 40942 AN XY: 74316

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.541

Alfa AF: 0.607 Hom.: 10044

Bravo AF: 0.532

Asia WGS AF: 0.536 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6736458; hg19: chr2-192023708;