rs16833177

chr2-191022906-T-C

Variant summary

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

The NR_136318.1(STAT4-AS1):n.30+1351T>C variant causes a intron, non coding transcript 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 NR_136318.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

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

LOC124900514 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAT4-AS1	NR_136318.1	n.30+1351T>C		intron_variant, non_coding_transcript_variant
LOC124900514	XR_007087796.1	n.802+1562T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAT4-AS1	ENST00000456176.5	n.30+1351T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.278

Alfa AF: 0.232 Hom.: 1046

Bravo AF: 0.271

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.5
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16833177; hg19: chr2-191887632;