Genetic Variant IL12A-AS1:n.166+500A>G (chr3-160015196-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 ENST00000462431.1(IL12A-AS1):n.166+500A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,094 control chromosomes in the GnomAD database, including 12,851 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 ( 12851 hom., cov: 33)

Consequence

IL12A-AS1
ENST00000462431.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.131

Publications

20 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1 link	n.583-5939A>G		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
IL12A-AS1	ENST00000462431.1 link	n.166+500A>G	intron_variant	Intron 1 of 4	5
IL12A-AS1	ENST00000497452.5 link	n.583-5939A>G	intron_variant	Intron 4 of 9	2
IL12A-AS1	ENST00000642756.1 link	n.367-5939A>G	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.407

AC:

61864

AN:

151976

Hom.:

12829

Cov.:

show subpopulations

Gnomad AFR

AF:

0.470

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.293

Gnomad EAS

AF:

0.213

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.363

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.367

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

GnomAD4 genome

AF:

0.407

AC:

61923

AN:

152094

Hom.:

12851

Cov.:

AF XY:

0.396

AC XY:

29438

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.470

AC:

19510

AN:

41486

American (AMR)

AF:

0.363

AC:

5547

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.293

AC:

1018

AN:

3470

East Asian (EAS)

AF:

0.213

AC:

1103

AN:

5176

South Asian (SAS)

AF:

0.221

AC:

1066

AN:

4824

European-Finnish (FIN)

AF:

0.363

AC:

3839

AN:

10566

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.421

AC:

28635

AN:

67966

Other (OTH)

AF:

0.367

AC:

777

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1902

3804

5707

7609

9511

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

580

1160

1740

2320

2900

<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:

0.409

Hom.:

53905

Bravo

AF:

0.416

Asia WGS

AF:

0.193

AC:

670

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.4

(source)

DANN

Benign

0.61

PhyloP100

0.13

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