rs11570915

Variant names:

• chr12-68225824-G-A
• rs11570915
• ENST00000536914.1:n.337-8705G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000536914.1(IFNG-AS1):​n.337-8705G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536914.1. 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
	IL26	NM_018402.2	MANE Select	c.-68C>T		upstream_gene	N/A	NP_060872.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG-AS1	ENST00000536914.1	TSL:5	n.337-8705G>A		intron	N/A
	IL26	ENST00000229134.5	TSL:1 MANE Select	c.-68C>T		upstream_gene	N/A	ENSP00000229134.4

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

African (AFR) AF: 0.0470 AC: 1448 AN: 30822

American (AMR) AF: 0.146 AC: 5989 AN: 41044

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 2453 AN: 23080

East Asian (EAS) AF: 0.0149 AC: 580 AN: 38996

South Asian (SAS) AF: 0.0973 AC: 7548 AN: 77602

European-Finnish (FIN) AF: 0.122 AC: 6281 AN: 51582

Middle Eastern (MID) AF: 0.102 AC: 553 AN: 5402

European-Non Finnish (NFE) AF: 0.124 AC: 125832 AN: 1016808

Other (OTH) AF: 0.107 AC: 6012 AN: 56014

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

African (AFR) AF: 0.0489 AC: 2032 AN: 41540

American (AMR) AF: 0.121 AC: 1854 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3468

East Asian (EAS) AF: 0.00771 AC: 40 AN: 5186

South Asian (SAS) AF: 0.0978 AC: 472 AN: 4828

European-Finnish (FIN) AF: 0.133 AC: 1406 AN: 10584

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8213 AN: 68006

Other (OTH) AF: 0.111 AC: 235 AN: 2112

Alfa AF: 0.114 Hom.: 590

Bravo AF: 0.0965

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		0.54
PromoterAI		0.0078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11570915; hg19: chr12-68619604;