chr12-68201364-T-C

Variant names:

• chr12-68201364-T-C
• rs3741809
• NM_018402.2:c.*481A>G

Variant summary

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

The NM_018402.2(IL26):​c.*481A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,638 control chromosomes in the GnomAD database, including 2,111 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 0.13 (2108 hom., cov: 32)
  • Exomes 𝑓: 0.088 (3 hom.)
• Consequence: IL26 NM_018402.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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)

LOC105369818 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL26	NM_018402.2	c.*481A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000229134.5	NP_060872.1
LOC105369818	XR_001749193.2	n.*11T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL26	ENST00000229134	c.*481A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_018402.2	ENSP00000229134.4
IFNG-AS1	ENST00000536914.1	n.337-33165T>C		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20352 AN: 152100 Hom.: 2100 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0839

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.0881 AC: 37 AN: 420 Hom.: 3 Cov.: 0 AF XY: 0.109 AC XY: 26 AN XY: 238

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.108

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.0593

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.134 AC: 20372 AN: 152218 Hom.: 2108 Cov.: 32 AF XY: 0.144 AC XY: 10688 AN XY: 74436

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0839

Gnomad4 OTH AF: 0.149

Alfa AF: 0.104 Hom.: 1134

Bravo AF: 0.145

Asia WGS AF: 0.312 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.62

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: rs3741809; hg19: chr12-68595144;