rs3024912

Variant names:

• chr2-191028361-A-C
• rs3024912
• ENST00000456176.5:n.31-2524A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456176.5(STAT4-AS1):​n.31-2524A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,014 control chromosomes in the GnomAD database, including 6,780 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 0.29 (6780 hom., cov: 32)
• Consequence: STAT4-AS1 ENST00000456176.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 23 publications found

Genes affected

STAT4-AS1 (HGNC:55764): (STAT4 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAT4-AS1	NR_136318.1	n.31-2524A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAT4-AS1	ENST00000456176.5	n.31-2524A>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43354 AN: 151896 Hom.: 6778 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.285 AC: 43387 AN: 152014 Hom.: 6780 Cov.: 32 AF XY: 0.285 AC XY: 21171 AN XY: 74318

African (AFR) AF: 0.398 AC: 16482 AN: 41442

American (AMR) AF: 0.238 AC: 3632 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3468

East Asian (EAS) AF: 0.484 AC: 2496 AN: 5156

South Asian (SAS) AF: 0.162 AC: 782 AN: 4816

European-Finnish (FIN) AF: 0.260 AC: 2750 AN: 10568

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15526 AN: 67972

Other (OTH) AF: 0.301 AC: 636 AN: 2110

Alfa AF: 0.242 Hom.: 8133

Bravo AF: 0.292

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.36
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs3024912; hg19: chr2-191893087;