rs2243115

Variant names:

• chr3-159988493-T-G
• rs2243115
• ENST00000497452.5:n.1350+604A>C

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+604A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,166 control chromosomes in the GnomAD database, including 865 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 0.10 (865 hom., cov: 32)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 77 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 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+604A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000497452.5	TSL:2	n.1350+604A>C		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.778+604A>C		intron	N/A
	IL12A-AS1	ENST00000654530.1		n.837+604A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15745 AN: 152048 Hom.: 863 Cov.: 32

Gnomad AFR AF: 0.0948

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0836

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.103 AC: 15740 AN: 152166 Hom.: 865 Cov.: 32 AF XY: 0.102 AC XY: 7593 AN XY: 74408

African (AFR) AF: 0.0946 AC: 3926 AN: 41522

American (AMR) AF: 0.0862 AC: 1318 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3472

East Asian (EAS) AF: 0.0836 AC: 432 AN: 5166

South Asian (SAS) AF: 0.121 AC: 582 AN: 4816

European-Finnish (FIN) AF: 0.106 AC: 1122 AN: 10602

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7690 AN: 67984

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.111 Hom.: 1637

Bravo AF: 0.100

Asia WGS AF: 0.114 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.045
DANN	Benign	0.42
PhyloP100		-2.4
PromoterAI		0.0049	Neutral
Mutation Taster		=100/0	polymorphism

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: rs2243115;

hg19: chr3-159706280;