rs3024908

Positions:

• chr2-191029415-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.31-1470T>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 0.0997 in 152,210 control chromosomes in the GnomAD database, including 826 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 0.10 (826 hom., cov: 32)
• Consequence: STAT4-AS1 NR_136318.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAT4-AS1	NR_136318.1	n.31-1470T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAT4-AS1	ENST00000456176.5	n.31-1470T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15173 AN: 152092 Hom.: 826 Cov.: 32

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0997 AC: 15177 AN: 152210 Hom.: 826 Cov.: 32 AF XY: 0.0977 AC XY: 7275 AN XY: 74428

Gnomad4 AFR AF: 0.0723

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.111

Alfa AF: 0.110 Hom.: 1956

Bravo AF: 0.100

Asia WGS AF: 0.125 AC: 435 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	0.36
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3024908; hg19: chr2-191894141;