dbSNP rs722749: IFNG-AS1:n.336+80150C>G (chr12-68106858-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000536914.1(IFNG-AS1):n.336+80150C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,996 control chromosomes in the GnomAD database, including 13,242 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 0.41 ( 13242 hom., cov: 32)

Consequence

IFNG-AS1
ENST00000536914.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.292

Publications

8 publications found

Variant links:

Genes affected

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

IFNG-AS1 links:

ENSG00000301254 (HGNC:):

ENSG00000301254 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
IFNG-AS1	ENST00000536914.1 link	n.336+80150C>G	intron_variant	Intron 5 of 5	5
ENSG00000301254	ENST00000777404.1 link	n.168-10887G>C	intron_variant	Intron 1 of 2
ENSG00000301254	ENST00000777405.1 link	n.188-10887G>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.406

AC:

61588

AN:

151878

Hom.:

13229

Cov.:

show subpopulations

Gnomad AFR

AF:

0.523

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.187

Gnomad FIN

AF:

0.382

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.405

Gnomad OTH

AF:

0.404

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

GnomAD4 genome

AF:

0.405

AC:

61634

AN:

151996

Hom.:

13242

Cov.:

AF XY:

0.396

AC XY:

29411

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.522

AC:

21650

AN:

41448

American (AMR)

AF:

0.294

AC:

4484

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

1214

AN:

3468

East Asian (EAS)

AF:

0.118

AC:

612

AN:

5172

South Asian (SAS)

AF:

0.188

AC:

908

AN:

4820

European-Finnish (FIN)

AF:

0.382

AC:

4039

AN:

10560

Middle Eastern (MID)

AF:

0.363

AC:

106

AN:

292

European-Non Finnish (NFE)

AF:

0.405

AC:

27506

AN:

67952

Other (OTH)

AF:

0.401

AC:

847

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1802

3604

5407

7209

9011

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

556

1112

1668

2224

2780

<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:

0.411

Hom.:

1607

Bravo

AF:

0.405

Asia WGS

AF:

0.206

AC:

720

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.3

(source)

DANN

Benign

0.70

PhyloP100

0.29

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over