rs2133310

Variant names:

• chr3-159998565-G-A
• rs2133310
• ENST00000462431.1:n.845-248C>T

Variant summary

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

The ENST00000497452.5(IL12A-AS1):​n.823-460C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,902 control chromosomes in the GnomAD database, including 14,896 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 0.43 (14896 hom., cov: 31)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.752
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.571 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	NR_108088.1		n.823-460C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000462431.1	TSL:5	n.845-248C>T		intron	N/A
	IL12A-AS1	ENST00000497452.5	TSL:2	n.823-460C>T		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.513-4260C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65435 AN: 151784 Hom.: 14878 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.431 AC: 65497 AN: 151902 Hom.: 14896 Cov.: 31 AF XY: 0.423 AC XY: 31379 AN XY: 74234

African (AFR) AF: 0.577 AC: 23893 AN: 41416

American (AMR) AF: 0.392 AC: 5982 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3472

East Asian (EAS) AF: 0.163 AC: 843 AN: 5166

South Asian (SAS) AF: 0.233 AC: 1121 AN: 4806

European-Finnish (FIN) AF: 0.379 AC: 3999 AN: 10546

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27227 AN: 67928

Other (OTH) AF: 0.408 AC: 862 AN: 2112

Alfa AF: 0.437 Hom.: 2450

Bravo AF: 0.445

Asia WGS AF: 0.232 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.8
DANN	Benign	0.69
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs2133310; hg19: chr3-159716352;