dbSNP rs4680536: IL12A-AS1:n.845-4167T>C (chr3-160002484-A-G) – 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.845-4167T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,036 control chromosomes in the GnomAD database, including 10,063 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 0.36 ( 10063 hom., cov: 32)

Consequence

IL12A-AS1
ENST00000462431.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.367

Publications

11 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1 link	n.823-4379T>C		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
IL12A-AS1	ENST00000462431.1 link	n.845-4167T>C	intron_variant	Intron 4 of 4	5
IL12A-AS1	ENST00000497452.5 link	n.823-4379T>C	intron_variant	Intron 6 of 9	2
IL12A-AS1	ENST00000642756.1 link	n.512+6628T>C	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.355

AC:

53978

AN:

151918

Hom.:

10060

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.285

Gnomad ASJ

AF:

0.289

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.395

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.432

Gnomad OTH

AF:

0.321

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

GnomAD4 genome

AF:

0.355

AC:

53998

AN:

152036

Hom.:

10063

Cov.:

AF XY:

0.347

AC XY:

25804

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.293

AC:

12162

AN:

41478

American (AMR)

AF:

0.285

AC:

4351

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.289

AC:

1002

AN:

3466

East Asian (EAS)

AF:

0.137

AC:

711

AN:

5180

South Asian (SAS)

AF:

0.227

AC:

1090

AN:

4806

European-Finnish (FIN)

AF:

0.395

AC:

4171

AN:

10556

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.432

AC:

29384

AN:

67940

Other (OTH)

AF:

0.321

AC:

678

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1738

3477

5215

6954

8692

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.393

Hom.:

15659

Bravo

AF:

0.347

Asia WGS

AF:

0.152

AC:

527

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.0

(source)

DANN

Benign

0.50

PhyloP100

0.37

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