rs4679868

Variant names:

• chr3-160006367-G-A
• rs4679868
• ENST00000462431.1:n.844+2745C>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+2745C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,054 control chromosomes in the GnomAD database, including 10,711 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 0.36 (10711 hom., cov: 32)
• Consequence: IL12A-AS1 ENST00000462431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.822+1415C>T		intron_variant	Intron 6 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000462431.1	n.844+2745C>T		intron_variant	Intron 4 of 4	5
IL12A-AS1	ENST00000497452.5	n.822+1415C>T		intron_variant	Intron 6 of 9	2
IL12A-AS1	ENST00000642756.1	n.512+2745C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55202 AN: 151936 Hom.: 10706 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.363 AC: 55210 AN: 152054 Hom.: 10711 Cov.: 32 AF XY: 0.372 AC XY: 27602 AN XY: 74296

African (AFR) AF: 0.220 AC: 9112 AN: 41472

American (AMR) AF: 0.472 AC: 7211 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1784 AN: 3470

East Asian (EAS) AF: 0.479 AC: 2474 AN: 5162

South Asian (SAS) AF: 0.412 AC: 1988 AN: 4824

European-Finnish (FIN) AF: 0.437 AC: 4621 AN: 10564

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26523 AN: 67980

Other (OTH) AF: 0.409 AC: 862 AN: 2108

Alfa AF: 0.386 Hom.: 3729

Bravo AF: 0.360

Asia WGS AF: 0.424 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs4679868; hg19: chr3-159724154;