3-159959585-C-T

Variant names:

• chr3-159959585-C-T
• rs34913294
• ENST00000497452.5:n.1350+29512G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000497452.5(IL12A-AS1):​n.1350+29512G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,174 control chromosomes in the GnomAD database, including 1,193 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 0.12 (1193 hom., cov: 32)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 1 publications found

Genes affected

IL12A-AS1 (HGNC:49094): (IL12A antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000497452.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	NR_108088.1		n.1350+29512G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000497452.5	TSL:2	n.1350+29512G>A		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.778+29512G>A		intron	N/A
	IL12A-AS1	ENST00000654530.1		n.837+29512G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17556 AN: 152056 Hom.: 1191 Cov.: 32

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.115 AC: 17563 AN: 152174 Hom.: 1193 Cov.: 32 AF XY: 0.115 AC XY: 8528 AN XY: 74404

African (AFR) AF: 0.0614 AC: 2552 AN: 41532

American (AMR) AF: 0.104 AC: 1585 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3470

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5188

South Asian (SAS) AF: 0.0565 AC: 272 AN: 4816

European-Finnish (FIN) AF: 0.159 AC: 1676 AN: 10570

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10188 AN: 67992

Other (OTH) AF: 0.123 AC: 260 AN: 2112

Alfa AF: 0.0509 Hom.: 63

Bravo AF: 0.109

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.65
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs34913294; hg19: chr3-159677373;