rs4679867

chr3-160006116-T-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.822+1666A>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 0.349 in 152,154 control chromosomes in the GnomAD database, including 9,633 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 0.35 (9633 hom., cov: 33)
• Consequence: IL12A-AS1 NR_108088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL12A-AS1	NR_108088.1	n.822+1666A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.822+1666A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53099 AN: 152036 Hom.: 9629 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.349 AC: 53122 AN: 152154 Hom.: 9633 Cov.: 33 AF XY: 0.340 AC XY: 25284 AN XY: 74390

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.319

Alfa AF: 0.399 Hom.: 1576

Bravo AF: 0.344

Asia WGS AF: 0.140 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.2
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4679867; hg19: chr3-159723903;