3-159998455-G-A

Variant names:

• chr3-159998455-G-A
• rs2243154
• ENST00000462431.1:n.845-138C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000462431.1(IL12A-AS1):​n.845-138C>T variant causes a intron 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 ENST00000462431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 17 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000462431.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	NR_108088.1		n.823-350C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000462431.1	TSL:5	n.845-138C>T		intron	N/A
	IL12A-AS1	ENST00000497452.5	TSL:2	n.823-350C>T		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.513-4150C>T		intron	N/A

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

African (AFR) AF: 0.0169 AC: 702 AN: 41564

American (AMR) AF: 0.0721 AC: 1103 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0810 AC: 281 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0193 AC: 93 AN: 4828

European-Finnish (FIN) AF: 0.0904 AC: 958 AN: 10602

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0882 AC: 5999 AN: 68016

Other (OTH) AF: 0.0743 AC: 157 AN: 2112

Alfa AF: 0.0605 Hom.: 287

Bravo AF: 0.0607

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs2243154; hg19: chr3-159716242;