dbSNP rs1353248: IL12A-AS1:n.1001-484G>A (chr3-159905770-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 ENST00000666425.1(IL12A-AS1):n.1001-484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,070 control chromosomes in the GnomAD database, including 8,209 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 0.32 ( 8209 hom., cov: 32)

Consequence

IL12A-AS1
ENST00000666425.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.283

Publications

16 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000666425.1 link	n.1001-484G>A		intron_variant	Intron 6 of 6
IL12A-AS1	ENST00000740375.1 link	n.625-484G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48406

AN:

151952

Hom.:

8185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.293

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

GnomAD4 genome

AF:

0.319

AC:

48470

AN:

152070

Hom.:

8209

Cov.:

AF XY:

0.316

AC XY:

23505

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.430

AC:

17846

AN:

41466

American (AMR)

AF:

0.213

AC:

3256

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

866

AN:

3462

East Asian (EAS)

AF:

0.226

AC:

1170

AN:

5170

South Asian (SAS)

AF:

0.227

AC:

1095

AN:

4824

European-Finnish (FIN)

AF:

0.318

AC:

3361

AN:

10570

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.292

AC:

19829

AN:

67974

Other (OTH)

AF:

0.293

AC:

621

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1673

3346

5019

6692

8365

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

482

964

1446

1928

2410

<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:

0.296

Hom.:

6380

Bravo

AF:

0.317

Asia WGS

AF:

0.239

AC:

831

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

3.1

(source)

DANN

Benign

0.57

PhyloP100

0.28

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