Genetic Variant ENST00000497452.5:n.1350+10952C>A (chr3-159978145-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000497452.5(IL12A-AS1):n.1350+10952C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,108 control chromosomes in the GnomAD database, including 1,858 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 0.14 ( 1858 hom., cov: 32)

Consequence

IL12A-AS1
ENST00000497452.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.464

Publications

6 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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1 link	n.1350+10952C>A		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
IL12A-AS1	ENST00000497452.5 link	n.1350+10952C>A	intron_variant	Intron 9 of 9	2
IL12A-AS1	ENST00000642756.1 link	n.778+10952C>A	intron_variant	Intron 4 of 4
IL12A-AS1	ENST00000654530.1 link	n.837+10952C>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

21904

AN:

151990

Hom.:

1850

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0480

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.156

Gnomad SAS

AF:

0.0870

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.183

Gnomad OTH

AF:

0.171

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

GnomAD4 genome

AF:

0.144

AC:

21934

AN:

152108

Hom.:

1858

Cov.:

AF XY:

0.142

AC XY:

10576

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.0481

AC:

1995

AN:

41496

American (AMR)

AF:

0.204

AC:

3118

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.222

AC:

770

AN:

3466

East Asian (EAS)

AF:

0.157

AC:

812

AN:

5186

South Asian (SAS)

AF:

0.0881

AC:

424

AN:

4814

European-Finnish (FIN)

AF:

0.163

AC:

1718

AN:

10558

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.183

AC:

12472

AN:

68000

Other (OTH)

AF:

0.177

AC:

373

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

954

1909

2863

3818

4772

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<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:

0.175

Hom.:

3496

Bravo

AF:

0.146

Asia WGS

AF:

0.113

AC:

392

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.11

(source)

DANN

Benign

0.83

PhyloP100

-0.46

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