Variant chr3-160015813-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_108088.1(IL12A-AS1):n.583-6556C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 279,006 control chromosomes in the GnomAD database, including 21,910 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 ( 12845 hom., cov: 32)

Exomes 𝑓: 0.36 ( 9065 hom. )

Consequence

IL12A-AS1
NR_108088.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.265

Variant links:

Genes affected

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

IL12A-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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/exons	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1 linkuse as main transcript	n.583-6556C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5 linkuse as main transcript	n.583-6556C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.407

AC:

61844

AN:

151848

Hom.:

12823

Cov.:

show subpopulations

Gnomad AFR

AF:

0.470

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.214

Gnomad SAS

AF:

0.222

Gnomad FIN

AF:

0.363

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.367

GnomAD4 exome

AF:

0.363

AC:

46083

AN:

127040

Hom.:

9065

Cov.:

AF XY:

0.344

AC XY:

24197

AN XY:

70250

show subpopulations

Gnomad4 AFR exome

AF:

0.471

Gnomad4 AMR exome

AF:

0.359

Gnomad4 ASJ exome

AF:

0.305

Gnomad4 EAS exome

AF:

0.204

Gnomad4 SAS exome

AF:

0.228

Gnomad4 FIN exome

AF:

0.366

Gnomad4 NFE exome

AF:

0.417

Gnomad4 OTH exome

AF:

0.365

GnomAD4 genome

AF:

0.407

AC:

61903

AN:

151966

Hom.:

12845

Cov.:

AF XY:

0.396

AC XY:

29428

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.470

Gnomad4 AMR

AF:

0.363

Gnomad4 ASJ

AF:

0.294

Gnomad4 EAS

AF:

0.214

Gnomad4 SAS

AF:

0.222

Gnomad4 FIN

AF:

0.363

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.368

Alfa

AF:

0.434

Hom.:

1830

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

-0.97

CADD

Benign

5.8

DANN

Benign

0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over