ENST00000456176.5:n.30+1351T>C

Variant names:

• chr2-191022906-T-C
• rs16833177
• ENST00000456176.5:n.30+1351T>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.30+1351T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,986 control chromosomes in the GnomAD database, including 5,910 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 0.26 (5910 hom., cov: 31)
• Consequence: STAT4-AS1 ENST00000456176.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 7 publications found

Genes affected

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

LOC124900514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456176.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAT4-AS1	NR_136318.1		n.30+1351T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAT4-AS1	ENST00000456176.5	TSL:5	n.30+1351T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39986 AN: 151870 Hom.: 5907 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.263 AC: 40018 AN: 151986 Hom.: 5910 Cov.: 31 AF XY: 0.264 AC XY: 19618 AN XY: 74286

African (AFR) AF: 0.389 AC: 16122 AN: 41426

American (AMR) AF: 0.222 AC: 3390 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3466

East Asian (EAS) AF: 0.426 AC: 2198 AN: 5160

South Asian (SAS) AF: 0.155 AC: 750 AN: 4826

European-Finnish (FIN) AF: 0.241 AC: 2550 AN: 10566

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13395 AN: 67958

Other (OTH) AF: 0.278 AC: 584 AN: 2104

Alfa AF: 0.239 Hom.: 1930

Bravo AF: 0.271

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.83
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs16833177; hg19: chr2-191887632;