rs2870946

chr12-68202881-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018402.2(IL26):c.364-798A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0688 in 152,214 control chromosomes in the GnomAD database, including 363 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 0.069 (363 hom., cov: 32)
• Consequence: IL26 NM_018402.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

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]

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL26	NM_018402.2	c.364-798A>G		intron_variant		ENST00000229134.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL26	ENST00000229134.5	c.364-798A>G		intron_variant		1	NM_018402.2	P1
IFNG-AS1	ENST00000536914.1	n.337-31648T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0687 AC: 10456 AN: 152096 Hom.: 363 Cov.: 32

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0374

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0688 AC: 10471 AN: 152214 Hom.: 363 Cov.: 32 AF XY: 0.0675 AC XY: 5028 AN XY: 74436

Gnomad4 AFR AF: 0.0971

Gnomad4 AMR AF: 0.0526

Gnomad4 ASJ AF: 0.0887

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0377

Gnomad4 FIN AF: 0.0665

Gnomad4 NFE AF: 0.0622

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0669 Hom.: 516

Bravo AF: 0.0706

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.85
Dann	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2870946; hg19: chr12-68596661;