rs13020076

Positions:

• chr2-191022317-A-G

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+762A>G 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 0.0498 in 152,276 control chromosomes in the GnomAD database, including 258 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 0.050 (258 hom., cov: 32)
• Consequence: STAT4-AS1 NR_136318.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAT4-AS1	NR_136318.1	n.30+762A>G		intron_variant, non_coding_transcript_variant
LOC124900514	XR_007087796.1	n.802+973A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAT4-AS1	ENST00000456176.5	n.30+762A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0498 AC: 7572 AN: 152158 Hom.: 257 Cov.: 32

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0529

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0736

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0498 AC: 7579 AN: 152276 Hom.: 258 Cov.: 32 AF XY: 0.0483 AC XY: 3596 AN XY: 74464

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.0528

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0230

Gnomad4 FIN AF: 0.0335

Gnomad4 NFE AF: 0.0736

Gnomad4 OTH AF: 0.0596

Alfa AF: 0.0587 Hom.: 29

Bravo AF: 0.0517

Asia WGS AF: 0.0130 AC: 47 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	2.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13020076; hg19: chr2-191887043;