rs1353248

Positions:

• chr3-159905770-C-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000666425.1	n.1001-484G>A		intron_variant, non_coding_transcript_variant

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;