rs9811792

Positions:

• chr3-159979210-C-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.1350+9887G>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 0.586 in 151,920 control chromosomes in the GnomAD database, including 26,725 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 0.59 (26725 hom., cov: 32)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.1350+9887G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1350+9887G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88900 AN: 151802 Hom.: 26686 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.586 AC: 88996 AN: 151920 Hom.: 26725 Cov.: 32 AF XY: 0.579 AC XY: 43021 AN XY: 74248

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.578

Alfa AF: 0.561 Hom.: 33026

Bravo AF: 0.586

Asia WGS AF: 0.487 AC: 1692 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9811792; hg19: chr3-159696998;