rs10878789

Positions:

• chr12-68210054-G-A
• chr12-68210054-G-T

Variant summary

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

The NM_018402.2(IL26):​c.364-7971C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 151,522 control chromosomes in the GnomAD database, including 3,315 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 0.18 (3315 hom., cov: 30)
• Consequence: IL26 NM_018402.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL26	NM_018402.2	c.364-7971C>T		intron_variant		ENST00000229134.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL26	ENST00000229134.5	c.364-7971C>T		intron_variant		1	NM_018402.2	P1
IFNG-AS1	ENST00000536914.1	n.337-24475G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27676 AN: 151402 Hom.: 3306 Cov.: 30

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0947

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.183 AC: 27704 AN: 151522 Hom.: 3315 Cov.: 30 AF XY: 0.194 AC XY: 14377 AN XY: 73984

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.198

Alfa AF: 0.139 Hom.: 3909

Bravo AF: 0.189

Asia WGS AF: 0.397 AC: 1377 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.57

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: rs10878789; hg19: chr12-68603834;