rs11570915

chr12-68225824-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000536914.1(IFNG-AS1):n.337-8705G>A 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 0.115 in 1,493,566 control chromosomes in the GnomAD database, including 10,505 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 0.097 (828 hom., cov: 32)
  • Exomes 𝑓: 0.12 (9677 hom.)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

Genes affected

IFNG-AS1 (HGNC:43910): (IFNG antisense RNA 1)

IL26 (HGNC:17119): (interleukin 26) This gene was identified by its overexpression specifically in herpesvirus samimiri-transformed T cells. The encoded protein is a member of the IL10 family of cytokines. It is a secreted protein and may function as a homodimer. This protein is thought to contribute to the transformed phenotype of T cells after infection by herpesvirus samimiri. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL26	NM_018402.2			upstream_gene_variant		ENST00000229134.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-8705G>A		intron_variant, non_coding_transcript_variant		5
IL26	ENST00000229134.5			upstream_gene_variant		1	NM_018402.2	P1

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14788 AN: 152098 Hom.: 830 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00770

Gnomad SAS AF: 0.0977

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.117 AC: 156696 AN: 1341350 Hom.: 9677 Cov.: 20 AF XY: 0.117 AC XY: 77951 AN XY: 669050

Gnomad4 AFR exome AF: 0.0470

Gnomad4 AMR exome AF: 0.146

Gnomad4 ASJ exome AF: 0.106

Gnomad4 EAS exome AF: 0.0149

Gnomad4 SAS exome AF: 0.0973

Gnomad4 FIN exome AF: 0.122

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.107

GnomAD4 genome AF: 0.0972 AC: 14793 AN: 152216 Hom.: 828 Cov.: 32 AF XY: 0.0979 AC XY: 7285 AN XY: 74422

Gnomad4 AFR AF: 0.0489

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.00771

Gnomad4 SAS AF: 0.0978

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.111

Alfa AF: 0.115 Hom.: 542

Bravo AF: 0.0965

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
Cadd	Benign	12
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: rs11570915; hg19: chr12-68619604;