rs2243148

Variant names:

• chr3-159997624-T-C
• rs2243148
• ENST00000660728.1:n.909A>G

Variant summary

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

The ENST00000660728.1(IL12A-AS1):​n.909A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,990 control chromosomes in the GnomAD database, including 3,958 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 0.21 (3958 hom., cov: 31)
• Consequence: IL12A-AS1 ENST00000660728.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 12 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 (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660728.1. 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.1084+220A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000660728.1		n.909A>G		non_coding_transcript_exon	Exon 3 of 3
	IL12A-AS1	ENST00000664175.2		n.866A>G		non_coding_transcript_exon	Exon 3 of 3
	IL12A-AS1	ENST00000671614.1		n.960A>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.211 AC: 31977 AN: 151874 Hom.: 3958 Cov.: 31

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.210 AC: 31989 AN: 151990 Hom.: 3958 Cov.: 31 AF XY: 0.206 AC XY: 15334 AN XY: 74280

African (AFR) AF: 0.0802 AC: 3326 AN: 41482

American (AMR) AF: 0.264 AC: 4029 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3472

East Asian (EAS) AF: 0.0786 AC: 407 AN: 5176

South Asian (SAS) AF: 0.113 AC: 544 AN: 4820

European-Finnish (FIN) AF: 0.270 AC: 2844 AN: 10526

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19345 AN: 67924

Other (OTH) AF: 0.216 AC: 457 AN: 2112

Alfa AF: 0.228 Hom.: 800

Bravo AF: 0.212

Asia WGS AF: 0.0940 AC: 328 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	0.83
DANN	Benign	0.70
PhyloP100		-0.42

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: rs2243148;

hg19: chr3-159715411;