rs2243149

Positions:

• chr3-159997925-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_108088.1(IL12A-AS1):​n.1003G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,964 control chromosomes in the GnomAD database, including 14,907 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 0.43 (14903 hom., cov: 32)
  • Exomes 𝑓: 0.40 (4 hom.)
• Consequence: IL12A-AS1 NR_108088.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL12A-AS1	NR_108088.1	n.1003G>A		non_coding_transcript_exon_variant	7/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1003G>A		non_coding_transcript_exon_variant	7/10	2

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65449 AN: 151806 Hom.: 14885 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.410

GnomAD4 exome AF: 0.400 AC: 16 AN: 40 Hom.: 4 Cov.: 0 AF XY: 0.357 AC XY: 10 AN XY: 28

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 0.385

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.431 AC: 65511 AN: 151924 Hom.: 14903 Cov.: 32 AF XY: 0.423 AC XY: 31401 AN XY: 74266

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.407

Alfa AF: 0.427 Hom.: 2736

Bravo AF: 0.445

Asia WGS AF: 0.232 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.34
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243149; hg19: chr3-159715712;