dbSNP rs3741809: IL26:c.*481A>G (chr12-68201364-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.122

Publications

7 publications found

Variant links:

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]

IL26 links:

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

IFNG-AS1 links:

LOC105369818 (HGNC:):

LOC105369818 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 link	c.*481A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000229134.5	NP_060872.1	Q9NPH9A0A7R8GUW8
LOC105369818	XR_001749193.2 link	n.*11T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL26	ENST00000229134.5 link	c.*481A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_018402.2	ENSP00000229134.4		Q9NPH9
IFNG-AS1	ENST00000536914.1 link	n.337-33165T>C		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20352

AN:

152100

Hom.:

2100

Cov.:

show subpopulations

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:

AN:

420

Hom.:

Cov.:

AF XY:

0.109

AC XY:

AN XY:

238

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.108

AC:

AN:

148

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0593

AC:

AN:

236

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.134

AC:

20372

AN:

152218

Hom.:

2108

Cov.:

AF XY:

0.144

AC XY:

10688

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.101

AC:

4213

AN:

41550

American (AMR)

AF:

0.278

AC:

4255

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.147

AC:

510

AN:

3472

East Asian (EAS)

AF:

0.483

AC:

2500

AN:

5178

South Asian (SAS)

AF:

0.264

AC:

1277

AN:

4828

European-Finnish (FIN)

AF:

0.143

AC:

1519

AN:

10590

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0839

AC:

5705

AN:

67994

Other (OTH)

AF:

0.149

AC:

316

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

838

1676

2515

3353

4191

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

226

452

678

904

1130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.104

Hom.:

1339

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

(source)

DANN

Benign

0.62

PhyloP100

-0.12

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over