chr3-159997599-A-G

Variant names:

• chr3-159997599-A-G
• rs2243147
• ENST00000664175.2:n.891T>C

Variant summary

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

The ENST00000664175.2(IL12A-AS1):​n.891T>C 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 0.426 in 151,536 control chromosomes in the GnomAD database, including 14,463 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 0.43 (14463 hom., cov: 30)
• Consequence: IL12A-AS1 ENST00000664175.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531
• Publications: 7 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664175.2. 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+245T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000664175.2		n.891T>C		non_coding_transcript_exon	Exon 3 of 3
	IL12A-AS1	ENST00000671614.1		n.985T>C		non_coding_transcript_exon	Exon 4 of 4
	IL12A-AS1	ENST00000740380.1		n.1071T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64568 AN: 151418 Hom.: 14445 Cov.: 30

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.426 AC: 64630 AN: 151536 Hom.: 14463 Cov.: 30 AF XY: 0.418 AC XY: 30933 AN XY: 74058

African (AFR) AF: 0.562 AC: 23169 AN: 41218

American (AMR) AF: 0.391 AC: 5965 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3468

East Asian (EAS) AF: 0.163 AC: 841 AN: 5170

South Asian (SAS) AF: 0.233 AC: 1120 AN: 4810

European-Finnish (FIN) AF: 0.374 AC: 3906 AN: 10446

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.401 AC: 27205 AN: 67882

Other (OTH) AF: 0.407 AC: 854 AN: 2098

Alfa AF: 0.423 Hom.: 2015

Bravo AF: 0.441

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.83
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2243147; hg19: chr3-159715386;