3-160015813-G-A

Variant names:

• chr3-160015813-G-A
• rs589545
• ENST00000462431.1:n.49C>T

Variant summary

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

The ENST00000462431.1(IL12A-AS1):​n.49C>T 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 0.387 in 279,006 control chromosomes in the GnomAD database, including 21,910 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 0.41 (12845 hom., cov: 32)
  • Exomes 𝑓: 0.36 (9065 hom.)
• Consequence: IL12A-AS1 ENST00000462431.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 8 publications found

Genes affected

IL12A-AS1 (HGNC:49094): (IL12A antisense RNA 1)

LINC01100 (HGNC:49224): (long intergenic non-protein coding RNA 1100)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000462431.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	NR_108088.1		n.583-6556C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000462431.1	TSL:5	n.49C>T		non_coding_transcript_exon	Exon 1 of 5
	IL12A-AS1	ENST00000497452.5	TSL:2	n.583-6556C>T		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.367-6556C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61844 AN: 151848 Hom.: 12823 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.367

GnomAD4 exome AF: 0.363 AC: 46083 AN: 127040 Hom.: 9065 Cov.: 0 AF XY: 0.344 AC XY: 24197 AN XY: 70250

African (AFR) AF: 0.471 AC: 939 AN: 1992

American (AMR) AF: 0.359 AC: 1678 AN: 4676

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 874 AN: 2870

East Asian (EAS) AF: 0.204 AC: 594 AN: 2914

South Asian (SAS) AF: 0.228 AC: 6150 AN: 26988

European-Finnish (FIN) AF: 0.366 AC: 2222 AN: 6076

Middle Eastern (MID) AF: 0.302 AC: 149 AN: 494

European-Non Finnish (NFE) AF: 0.417 AC: 31177 AN: 74734

Other (OTH) AF: 0.365 AC: 2300 AN: 6296

GnomAD4 genome AF: 0.407 AC: 61903 AN: 151966 Hom.: 12845 Cov.: 32 AF XY: 0.396 AC XY: 29428 AN XY: 74262

African (AFR) AF: 0.470 AC: 19509 AN: 41470

American (AMR) AF: 0.363 AC: 5533 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3466

East Asian (EAS) AF: 0.214 AC: 1104 AN: 5156

South Asian (SAS) AF: 0.222 AC: 1068 AN: 4818

European-Finnish (FIN) AF: 0.363 AC: 3825 AN: 10528

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28643 AN: 67974

Other (OTH) AF: 0.368 AC: 774 AN: 2106

Alfa AF: 0.436 Hom.: 1916

Bravo AF: 0.416

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.8
DANN	Benign	0.80
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs589545; hg19: chr3-159733600;