3-159926508-A-G

Position:

• chr3-159926508-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.1351-12034T>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 0.177 in 152,174 control chromosomes in the GnomAD database, including 2,636 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 0.18 (2636 hom., cov: 32)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL12A-AS1	NR_108088.1	n.1351-12034T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1351-12034T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26970 AN: 152056 Hom.: 2634 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.177 AC: 26992 AN: 152174 Hom.: 2636 Cov.: 32 AF XY: 0.178 AC XY: 13238 AN XY: 74396

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0891

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.184

Alfa AF: 0.209 Hom.: 4699

Bravo AF: 0.172

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6799788; hg19: chr3-159644297;