3-160001345-A-G

Variant names:

• chr3-160001345-A-G
• rs485497
• ENST00000462431.1:n.845-3028T>C

Variant summary

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

The ENST00000497452.5(IL12A-AS1):​n.823-3240T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,954 control chromosomes in the GnomAD database, including 25,659 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 0.56 (25659 hom., cov: 32)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 41 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 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.823-3240T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000462431.1	TSL:5	n.845-3028T>C		intron	N/A
	IL12A-AS1	ENST00000497452.5	TSL:2	n.823-3240T>C		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.513-7040T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84967 AN: 151836 Hom.: 25614 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.560 AC: 85071 AN: 151954 Hom.: 25659 Cov.: 32 AF XY: 0.550 AC XY: 40839 AN XY: 74240

African (AFR) AF: 0.794 AC: 32940 AN: 41470

American (AMR) AF: 0.402 AC: 6130 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1190 AN: 5160

South Asian (SAS) AF: 0.502 AC: 2414 AN: 4808

European-Finnish (FIN) AF: 0.452 AC: 4773 AN: 10560

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.509 AC: 34564 AN: 67922

Other (OTH) AF: 0.504 AC: 1062 AN: 2106

Alfa AF: 0.514 Hom.: 34904

Bravo AF: 0.562

Asia WGS AF: 0.442 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.62
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs485497; hg19: chr3-159719132;