rs4853551

chr2-191166537-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+6047A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,216 control chromosomes in the GnomAD database, including 55,363 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 0.84 (55363 hom., cov: 32)
• Consequence: STAT4 XM_047445600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

STAT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4	XM_047445600.1	c.26+6047A>G		intron_variant
STAT4	XM_047445601.1	c.26+6047A>G		intron_variant
STAT4	XM_047445602.1	c.26+6047A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128477 AN: 152098 Hom.: 55342 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.844 AC: 128539 AN: 152216 Hom.: 55363 Cov.: 32 AF XY: 0.848 AC XY: 63114 AN XY: 74412

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.915

Gnomad4 OTH AF: 0.863

Alfa AF: 0.899 Hom.: 63169

Bravo AF: 0.833

Asia WGS AF: 0.888 AC: 3090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	14
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4853551; hg19: chr2-192031263;