chr3-159998565-G-A

Position:

• chr3-159998565-G-A

Variant summary

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

The NR_108088.1(IL12A-AS1):​n.823-460C>T 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 0.431 in 151,902 control chromosomes in the GnomAD database, including 14,896 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 0.43 (14896 hom., cov: 31)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.752

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.823-460C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.823-460C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65435 AN: 151784 Hom.: 14878 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.431 AC: 65497 AN: 151902 Hom.: 14896 Cov.: 31 AF XY: 0.423 AC XY: 31379 AN XY: 74234

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.408

Alfa AF: 0.433 Hom.: 2320

Bravo AF: 0.445

Asia WGS AF: 0.232 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2133310; hg19: chr3-159716352;