2-191159824-T-C

Position:

• chr2-191159824-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.27-11620A>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 151,802 control chromosomes in the GnomAD database, including 24,901 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 (24901 hom., cov: 30)
• Consequence: STAT4 XM_047445600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649

Genes affected

STAT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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	Protein	UniProt
STAT4	XM_047445600.1	c.27-11620A>G		intron_variant			XP_047301556.1
STAT4	XM_047445601.1	c.27-11620A>G		intron_variant			XP_047301557.1
STAT4	XM_047445602.1	c.27-11620A>G		intron_variant			XP_047301558.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84336 AN: 151684 Hom.: 24886 Cov.: 30

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.503

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: 84397 AN: 151802 Hom.: 24901 Cov.: 30 AF XY: 0.563 AC XY: 41744 AN XY: 74178

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.548

Alfa AF: 0.604 Hom.: 3524

Bravo AF: 0.544

Asia WGS AF: 0.542 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16833453; hg19: chr2-192024550;