3-159996563-A-T

Position:

• chr3-159996563-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+1281T>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 0.402 in 151,968 control chromosomes in the GnomAD database, including 12,622 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 0.40 (12622 hom., cov: 31)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.1084+1281T>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.1084+1281T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61054 AN: 151850 Hom.: 12609 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.402 AC: 61101 AN: 151968 Hom.: 12622 Cov.: 31 AF XY: 0.394 AC XY: 29287 AN XY: 74288

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.392

Alfa AF: 0.402 Hom.: 1681

Bravo AF: 0.413

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
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: rs2243138; hg19: chr3-159714350;