3-159981731-G-T

Variant names:

• chr3-159981731-G-T
• rs747825
• ENST00000497452.5:n.1350+7366C>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+7366C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 151,952 control chromosomes in the GnomAD database, including 1,866 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 0.15 (1866 hom., cov: 33)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 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+7366C>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+7366C>A		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.778+7366C>A		intron	N/A
	IL12A-AS1	ENST00000654530.1		n.837+7366C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22252 AN: 151834 Hom.: 1859 Cov.: 33

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.147 AC: 22276 AN: 151952 Hom.: 1866 Cov.: 33 AF XY: 0.144 AC XY: 10733 AN XY: 74282

African (AFR) AF: 0.0569 AC: 2356 AN: 41436

American (AMR) AF: 0.201 AC: 3070 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3468

East Asian (EAS) AF: 0.158 AC: 814 AN: 5166

South Asian (SAS) AF: 0.0871 AC: 419 AN: 4812

European-Finnish (FIN) AF: 0.174 AC: 1830 AN: 10534

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12378 AN: 67938

Other (OTH) AF: 0.176 AC: 370 AN: 2106

Alfa AF: 0.0768 Hom.: 131

Bravo AF: 0.148

Asia WGS AF: 0.111 AC: 384 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.26
PhyloP100		0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs747825;

hg19: chr3-159699519;