chr3-159996563-A-T

Variant names:

• chr3-159996563-A-T
• rs2243138
• ENST00000497452.5:n.1084+1281T>A

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+1281T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,968 control chromosomes in the GnomAD database, including 12,622 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 0.40 (12622 hom., cov: 31)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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+1281T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000497452.5	TSL:2	n.1084+1281T>A		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.513-2258T>A		intron	N/A
	IL12A-AS1	ENST00000654530.1		n.571+1281T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61054 AN: 151850 Hom.: 12609 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.402 AC: 61101 AN: 151968 Hom.: 12622 Cov.: 31 AF XY: 0.394 AC XY: 29287 AN XY: 74288

African (AFR) AF: 0.473 AC: 19602 AN: 41438

American (AMR) AF: 0.385 AC: 5890 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3468

East Asian (EAS) AF: 0.164 AC: 846 AN: 5154

South Asian (SAS) AF: 0.233 AC: 1120 AN: 4812

European-Finnish (FIN) AF: 0.378 AC: 3999 AN: 10566

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27249 AN: 67940

Other (OTH) AF: 0.392 AC: 827 AN: 2110

Alfa AF: 0.402 Hom.: 1681

Bravo AF: 0.413

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.25
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2243138; hg19: chr3-159714350;