3-159996760-T-C

Variant names:

• chr3-159996760-T-C
• rs2243140
• ENST00000497452.5:n.1084+1084A>G

Variant summary

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

The ENST00000497452.5(IL12A-AS1):​n.1084+1084A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,056 control chromosomes in the GnomAD database, including 4,460 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 0.23 (4460 hom., cov: 31)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000497452.5. 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.1084+1084A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000497452.5	TSL:2	n.1084+1084A>G		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.513-2455A>G		intron	N/A
	IL12A-AS1	ENST00000654530.1		n.571+1084A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35669 AN: 151938 Hom.: 4461 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.235 AC: 35688 AN: 152056 Hom.: 4460 Cov.: 31 AF XY: 0.230 AC XY: 17092 AN XY: 74320

African (AFR) AF: 0.163 AC: 6780 AN: 41478

American (AMR) AF: 0.272 AC: 4162 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3472

East Asian (EAS) AF: 0.0792 AC: 410 AN: 5178

South Asian (SAS) AF: 0.115 AC: 553 AN: 4812

European-Finnish (FIN) AF: 0.272 AC: 2870 AN: 10560

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19381 AN: 67960

Other (OTH) AF: 0.234 AC: 494 AN: 2108

Alfa AF: 0.258 Hom.: 634

Bravo AF: 0.241

Asia WGS AF: 0.0980 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.70
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2243140; hg19: chr3-159714547;