chr2-191170317-T-C

Position:

• chr2-191170317-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.26+2267A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,990 control chromosomes in the GnomAD database, including 15,843 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 0.39 (15843 hom., cov: 32)
• Consequence: STAT4 XM_047445600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

Genes affected

STAT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAT4	XM_047445600.1	c.26+2267A>G		intron_variant			XP_047301556.1
STAT4	XM_047445601.1	c.26+2267A>G		intron_variant			XP_047301557.1
STAT4	XM_047445602.1	c.26+2267A>G		intron_variant			XP_047301558.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59700 AN: 151872 Hom.: 15791 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.394 AC: 59814 AN: 151990 Hom.: 15843 Cov.: 32 AF XY: 0.386 AC XY: 28699 AN XY: 74288

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.372

Alfa AF: 0.322 Hom.: 1357

Bravo AF: 0.415

Asia WGS AF: 0.396 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10176621; hg19: chr2-192035043;