rs2243147

chr3-159997599-A-Gchr3-159997599-A-T

Variant summary

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

The NR_108088.1(IL12A-AS1):n.1084+245T>C 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 0.426 in 151,536 control chromosomes in the GnomAD database, including 14,463 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 (14463 hom., cov: 30)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL12A-AS1	NR_108088.1	n.1084+245T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1084+245T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64568 AN: 151418 Hom.: 14445 Cov.: 30

Gnomad AFR AF: 0.562

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: 0.374

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.426 AC: 64630 AN: 151536 Hom.: 14463 Cov.: 30 AF XY: 0.418 AC XY: 30933 AN XY: 74058

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.407

Alfa AF: 0.423 Hom.: 2015

Bravo AF: 0.441

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	7.0
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243147; hg19: chr3-159715386;