rs897200

Positions:

• chr2-191153045-T-C
• chr2-191153045-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047445600.1(STAT4):​c.27-4841A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 152,036 control chromosomes in the GnomAD database, including 24,147 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 (24147 hom., cov: 32)
• Consequence: STAT4 XM_047445600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

Genes affected

STAT4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4	XM_047445600.1	c.27-4841A>G		intron_variant
STAT4	XM_047445601.1	c.27-4841A>G		intron_variant
STAT4	XM_047445602.1	c.27-4841A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82097 AN: 151918 Hom.: 24138 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.540 AC: 82135 AN: 152036 Hom.: 24147 Cov.: 32 AF XY: 0.546 AC XY: 40607 AN XY: 74304

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.539

Alfa AF: 0.559 Hom.: 5217

Bravo AF: 0.527

Asia WGS AF: 0.536 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs897200; hg19: chr2-192017771;