12-68226033-G-A

Variant names:

• chr12-68226033-G-A
• rs3814240
• ENST00000536914.1:n.337-8496G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536914.1(IFNG-AS1):​n.337-8496G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,028 control chromosomes in the GnomAD database, including 25,027 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 0.56 (25027 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 7 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL26	NM_018402.2	c.-277C>T		upstream_gene_variant		ENST00000229134.5	NP_060872.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-8496G>A		intron_variant	Intron 5 of 5	5
IL26	ENST00000229134.5	c.-277C>T		upstream_gene_variant		1	NM_018402.2	ENSP00000229134.4

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85334 AN: 151910 Hom.: 25000 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.0746

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.562 AC: 85397 AN: 152028 Hom.: 25027 Cov.: 32 AF XY: 0.551 AC XY: 40948 AN XY: 74304

African (AFR) AF: 0.673 AC: 27909 AN: 41476

American (AMR) AF: 0.500 AC: 7637 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1823 AN: 3472

East Asian (EAS) AF: 0.0750 AC: 388 AN: 5176

South Asian (SAS) AF: 0.496 AC: 2392 AN: 4826

European-Finnish (FIN) AF: 0.436 AC: 4594 AN: 10544

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38830 AN: 67954

Other (OTH) AF: 0.541 AC: 1142 AN: 2112

Alfa AF: 0.569 Hom.: 14215

Bravo AF: 0.568

Asia WGS AF: 0.336 AC: 1171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.64
PhyloP100		-0.13
PromoterAI		-0.0058	Neutral
Mutation Taster		=17/83	disease causing

Splicing

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

Other links and lift over

dbSNP: rs3814240; hg19: chr12-68619813;