3-159999842-T-G

Variant names:

• chr3-159999842-T-G
• rs17826053
• ENST00000462431.1:n.845-1525A>C

Variant summary

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

The ENST00000462431.1(IL12A-AS1):​n.845-1525A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,140 control chromosomes in the GnomAD database, including 1,919 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 0.15 (1919 hom., cov: 32)
• Consequence: IL12A-AS1 ENST00000462431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 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.823-1737A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000462431.1	TSL:5	n.845-1525A>C		intron	N/A
	IL12A-AS1	ENST00000497452.5	TSL:2	n.823-1737A>C		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.513-5537A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23015 AN: 152022 Hom.: 1919 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.151 AC: 23042 AN: 152140 Hom.: 1919 Cov.: 32 AF XY: 0.153 AC XY: 11370 AN XY: 74364

African (AFR) AF: 0.180 AC: 7451 AN: 41496

American (AMR) AF: 0.0857 AC: 1310 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3468

East Asian (EAS) AF: 0.129 AC: 668 AN: 5186

South Asian (SAS) AF: 0.324 AC: 1560 AN: 4818

European-Finnish (FIN) AF: 0.138 AC: 1455 AN: 10566

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9826 AN: 67998

Other (OTH) AF: 0.126 AC: 265 AN: 2110

Alfa AF: 0.164 Hom.: 332

Bravo AF: 0.141

Asia WGS AF: 0.245 AC: 849 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.77
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs17826053; hg19: chr3-159717629;