rs2243154

Positions:

• chr3-159998455-G-A
• chr3-159998455-G-C
• chr3-159998455-G-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.823-350C>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 0.0615 in 152,276 control chromosomes in the GnomAD database, including 382 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 0.061 (382 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.823-350C>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.823-350C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9357 AN: 152158 Hom.: 382 Cov.: 32

Gnomad AFR AF: 0.0169

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0882

Gnomad OTH AF: 0.0751

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

GnomAD4 genome AF: 0.0615 AC: 9360 AN: 152276 Hom.: 382 Cov.: 32 AF XY: 0.0609 AC XY: 4535 AN XY: 74442

Gnomad4 AFR AF: 0.0169

Gnomad4 AMR AF: 0.0721

Gnomad4 ASJ AF: 0.0810

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.0904

Gnomad4 NFE AF: 0.0882

Gnomad4 OTH AF: 0.0743

Alfa AF: 0.0635 Hom.: 174

Bravo AF: 0.0607

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243154; hg19: chr3-159716242;