rs17810546

Positions:

• chr3-159947262-A-G

Variant summary

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

The NR_108088.1(IL12A-AS1):​n.1351-32788T>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 0.0816 in 152,302 control chromosomes in the GnomAD database, including 670 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 0.082 (670 hom., cov: 32)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.1351-32788T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1351-32788T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12415 AN: 152184 Hom.: 668 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0816 AC: 12428 AN: 152302 Hom.: 670 Cov.: 32 AF XY: 0.0787 AC XY: 5861 AN XY: 74474

Gnomad4 AFR AF: 0.0226

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0391

Gnomad4 FIN AF: 0.0908

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0752

Alfa AF: 0.106 Hom.: 2030

Bravo AF: 0.0820

Asia WGS AF: 0.0180 AC: 63 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17810546; hg19: chr3-159665050;