rs589545

Positions:

• chr3-160015813-G-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265

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=-0.97).
• 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	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	n.583-6556C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61844 AN: 151848 Hom.: 12823 Cov.: 32

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.: 0 AF XY: 0.344 AC XY: 24197 AN XY: 70250

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.: 32 AF XY: 0.396 AC XY: 29428 AN XY: 74262

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

Other links and lift over

dbSNP: rs589545; hg19: chr3-159733600;