Genetic Variant IL12A-AS1:n.167-922G>A (chr3-160013032-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000462431.1(IL12A-AS1):n.167-922G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,922 control chromosomes in the GnomAD database, including 10,868 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 0.37 ( 10868 hom., cov: 32)

Consequence

IL12A-AS1
ENST00000462431.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

Publications

3 publications found

Variant links:

Genes affected

IL12A-AS1 (HGNC:49094): (IL12A antisense RNA 1)

IL12A-AS1 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1 link	n.583-3775G>A		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
IL12A-AS1	ENST00000462431.1 link	n.167-922G>A	intron_variant	Intron 1 of 4	5
IL12A-AS1	ENST00000497452.5 link	n.583-3775G>A	intron_variant	Intron 4 of 9	2
IL12A-AS1	ENST00000642756.1 link	n.367-3775G>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

55666

AN:

151804

Hom.:

10862

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.570

Gnomad AMR

AF:

0.473

Gnomad ASJ

AF:

0.513

Gnomad EAS

AF:

0.479

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.439

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.394

Gnomad OTH

AF:

0.416

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

GnomAD4 genome

AF:

0.366

AC:

55674

AN:

151922

Hom.:

10868

Cov.:

AF XY:

0.374

AC XY:

27805

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.225

AC:

9307

AN:

41428

American (AMR)

AF:

0.473

AC:

7217

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.513

AC:

1780

AN:

3468

East Asian (EAS)

AF:

0.479

AC:

2476

AN:

5170

South Asian (SAS)

AF:

0.415

AC:

1997

AN:

4808

European-Finnish (FIN)

AF:

0.439

AC:

4620

AN:

10530

Middle Eastern (MID)

AF:

0.391

AC:

115

AN:

294

European-Non Finnish (NFE)

AF:

0.394

AC:

26781

AN:

67956

Other (OTH)

AF:

0.411

AC:

865

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1748

3496

5243

6991

8739

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

540

1080

1620

2160

2700

<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:

0.337

Hom.:

2606

Bravo

AF:

0.363

Asia WGS

AF:

0.425

AC:

1481

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.3

(source)

DANN

Benign

0.40

PhyloP100

0.21

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