3-159997764-G-A

Variant names:

• chr3-159997764-G-A
• rs668998
• ENST00000660728.1:n.769C>T

Variant summary

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

The ENST00000660728.1(IL12A-AS1):​n.769C>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 0.621 in 151,982 control chromosomes in the GnomAD database, including 30,689 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 0.62 (30683 hom., cov: 31)
  • Exomes 𝑓: 0.75 (6 hom.)
• Consequence: IL12A-AS1 ENST00000660728.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 24 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	NR_108088.1		n.1084+80C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000660728.1		n.769C>T		non_coding_transcript_exon	Exon 3 of 3
	IL12A-AS1	ENST00000664175.2		n.726C>T		non_coding_transcript_exon	Exon 3 of 3
	IL12A-AS1	ENST00000671614.1		n.820C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94253 AN: 151848 Hom.: 30639 Cov.: 31

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.573

GnomAD4 exome AF: 0.750 AC: 12 AN: 16 Hom.: 6 AF XY: 0.667 AC XY: 8 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 8 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.621 AC: 94359 AN: 151966 Hom.: 30683 Cov.: 31 AF XY: 0.613 AC XY: 45551 AN XY: 74276

African (AFR) AF: 0.827 AC: 34317 AN: 41478

American (AMR) AF: 0.509 AC: 7771 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1952 AN: 3464

East Asian (EAS) AF: 0.294 AC: 1521 AN: 5172

South Asian (SAS) AF: 0.574 AC: 2762 AN: 4814

European-Finnish (FIN) AF: 0.523 AC: 5514 AN: 10544

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38640 AN: 67916

Other (OTH) AF: 0.575 AC: 1212 AN: 2106

Alfa AF: 0.581 Hom.: 101173

Bravo AF: 0.627

Asia WGS AF: 0.493 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.47
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs668998; hg19: chr3-159715551; COSMIC: COSV59759410;