12-68226017-G-T

Variant names:

• chr12-68226017-G-T
• rs3814241
• ENST00000536914.1:n.337-8512G>T

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-8512G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 150,744 control chromosomes in the GnomAD database, including 2,809 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 0.16 (2809 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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.-261C>A		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.337-8512G>T		intron	N/A
	IL26	ENST00000229134.5	TSL:1 MANE Select	c.-261C>A		upstream_gene	N/A	ENSP00000229134.4

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24532 AN: 150628 Hom.: 2800 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0956

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.163 AC: 24566 AN: 150744 Hom.: 2809 Cov.: 32 AF XY: 0.174 AC XY: 12815 AN XY: 73604

African (AFR) AF: 0.162 AC: 6690 AN: 41406

American (AMR) AF: 0.277 AC: 4176 AN: 15062

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 473 AN: 3448

East Asian (EAS) AF: 0.556 AC: 2872 AN: 5170

South Asian (SAS) AF: 0.203 AC: 965 AN: 4762

European-Finnish (FIN) AF: 0.237 AC: 2455 AN: 10364

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0956 AC: 6430 AN: 67256

Other (OTH) AF: 0.172 AC: 359 AN: 2082

Alfa AF: 0.106 Hom.: 671

Bravo AF: 0.170

Asia WGS AF: 0.381 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.70
PhyloP100		0.40
PromoterAI		-0.0032	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3814241; hg19: chr12-68619797;