chr3-160006116-T-A

Variant names:

• chr3-160006116-T-A
• rs4679867
• ENST00000462431.1:n.844+2996A>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.844+2996A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,154 control chromosomes in the GnomAD database, including 9,633 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 0.35 (9633 hom., cov: 33)
• Consequence: IL12A-AS1 ENST00000462431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 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.822+1666A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000462431.1	TSL:5	n.844+2996A>T		intron	N/A
	IL12A-AS1	ENST00000497452.5	TSL:2	n.822+1666A>T		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.512+2996A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53099 AN: 152036 Hom.: 9629 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.349 AC: 53122 AN: 152154 Hom.: 9633 Cov.: 33 AF XY: 0.340 AC XY: 25284 AN XY: 74390

African (AFR) AF: 0.312 AC: 12959 AN: 41504

American (AMR) AF: 0.279 AC: 4266 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3470

East Asian (EAS) AF: 0.137 AC: 710 AN: 5186

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4822

European-Finnish (FIN) AF: 0.362 AC: 3833 AN: 10584

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.416 AC: 28262 AN: 67982

Other (OTH) AF: 0.319 AC: 674 AN: 2114

Alfa AF: 0.399 Hom.: 1576

Bravo AF: 0.344

Asia WGS AF: 0.140 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.77
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs4679867; hg19: chr3-159723903;