rs2561288

chr3-159957140-T-C

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+31957A>G 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 0.536 in 151,984 control chromosomes in the GnomAD database, including 22,367 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 0.54 (22367 hom., cov: 32)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL12A-AS1	NR_108088.1	n.1350+31957A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1350+31957A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81418 AN: 151864 Hom.: 22321 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.536 AC: 81526 AN: 151984 Hom.: 22367 Cov.: 32 AF XY: 0.530 AC XY: 39378 AN XY: 74272

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.544

Alfa AF: 0.555 Hom.: 5174

Bravo AF: 0.542

Asia WGS AF: 0.412 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.6
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2561288; hg19: chr3-159674928;