rs1353248

Variant names:

• chr3-159905770-C-T
• rs1353248
• ENST00000666425.1:n.1001-484G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000666425.1(IL12A-AS1):​n.1001-484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,070 control chromosomes in the GnomAD database, including 8,209 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 0.32 (8209 hom., cov: 32)
• Consequence: IL12A-AS1 ENST00000666425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

IL12A-AS1 (HGNC:49094): (IL12A antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000666425.1	n.1001-484G>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48406 AN: 151952 Hom.: 8185 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.319 AC: 48470 AN: 152070 Hom.: 8209 Cov.: 32 AF XY: 0.316 AC XY: 23505 AN XY: 74342

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.293

Alfa AF: 0.295 Hom.: 5454

Bravo AF: 0.317

Asia WGS AF: 0.239 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1353248; hg19: chr3-159623559;