3-159978311-G-T

Variant names:

• chr3-159978311-G-T
• rs2366408
• ENST00000497452.5:n.1350+10786C>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+10786C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,480 control chromosomes in the GnomAD database, including 10,066 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 0.36 (10066 hom., cov: 31)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 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+10786C>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+10786C>A		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.778+10786C>A		intron	N/A
	IL12A-AS1	ENST00000654530.1		n.837+10786C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54175 AN: 151364 Hom.: 10037 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.358 AC: 54264 AN: 151480 Hom.: 10066 Cov.: 31 AF XY: 0.352 AC XY: 26082 AN XY: 73992

African (AFR) AF: 0.429 AC: 17710 AN: 41304

American (AMR) AF: 0.343 AC: 5206 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1697 AN: 3452

East Asian (EAS) AF: 0.160 AC: 828 AN: 5164

South Asian (SAS) AF: 0.156 AC: 748 AN: 4804

European-Finnish (FIN) AF: 0.336 AC: 3519 AN: 10462

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23207 AN: 67816

Other (OTH) AF: 0.382 AC: 803 AN: 2102

Alfa AF: 0.345 Hom.: 33324

Bravo AF: 0.367

Asia WGS AF: 0.188 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.43
DANN	Benign	0.52
PhyloP100		0.0040

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: rs2366408;

hg19: chr3-159696099;