3-160091667-C-G

Variant names:

• chr3-160091667-C-G
• rs937478
• ENST00000497452.5:n.518-66133G>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.518-66133G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 152,044 control chromosomes in the GnomAD database, including 30,967 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 0.63 (30967 hom., cov: 32)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.518-66133G>C		intron_variant	Intron 3 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.518-66133G>C		intron_variant	Intron 3 of 9	2

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95862 AN: 151926 Hom.: 30965 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.631 AC: 95875 AN: 152044 Hom.: 30967 Cov.: 32 AF XY: 0.632 AC XY: 46994 AN XY: 74300

African (AFR) AF: 0.476 AC: 19728 AN: 41438

American (AMR) AF: 0.735 AC: 11227 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2583 AN: 3470

East Asian (EAS) AF: 0.686 AC: 3549 AN: 5170

South Asian (SAS) AF: 0.669 AC: 3224 AN: 4818

European-Finnish (FIN) AF: 0.599 AC: 6333 AN: 10566

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47033 AN: 67986

Other (OTH) AF: 0.684 AC: 1443 AN: 2110

Alfa AF: 0.521 Hom.: 1523

Bravo AF: 0.632

Asia WGS AF: 0.623 AC: 2168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs937478; hg19: chr3-159809454;