rs12467660

chr2-191166924-A-Cchr2-191166924-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.26+5660T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,146 control chromosomes in the GnomAD database, including 47,604 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 0.77 (47604 hom., cov: 31)
• Consequence: STAT4 XM_047445600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

Genes affected

STAT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4	XM_047445600.1	c.26+5660T>G		intron_variant
STAT4	XM_047445601.1	c.26+5660T>G		intron_variant
STAT4	XM_047445602.1	c.26+5660T>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117671 AN: 152028 Hom.: 47584 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.774 AC: 117733 AN: 152146 Hom.: 47604 Cov.: 31 AF XY: 0.781 AC XY: 58151 AN XY: 74422

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.789

Alfa AF: 0.822 Hom.: 9814

Bravo AF: 0.755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.5
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12467660; hg19: chr2-192031650;