rs6441286

Variant names:

• chr3-160011091-T-G
• rs6441286
• ENST00000462431.1:n.698+375A>C

Variant summary

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

The ENST00000497452.5(IL12A-AS1):​n.583-1834A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,072 control chromosomes in the GnomAD database, including 10,766 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 (10766 hom., cov: 33)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 33 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000497452.5. 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.583-1834A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL12A-AS1	ENST00000462431.1	TSL:5	n.698+375A>C		intron	N/A
	IL12A-AS1	ENST00000497452.5	TSL:2	n.583-1834A>C		intron	N/A
	IL12A-AS1	ENST00000642756.1		n.367-1834A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55429 AN: 151954 Hom.: 10760 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.365 AC: 55437 AN: 152072 Hom.: 10766 Cov.: 33 AF XY: 0.373 AC XY: 27699 AN XY: 74332

African (AFR) AF: 0.224 AC: 9284 AN: 41510

American (AMR) AF: 0.473 AC: 7219 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1783 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2468 AN: 5164

South Asian (SAS) AF: 0.414 AC: 1994 AN: 4816

European-Finnish (FIN) AF: 0.438 AC: 4618 AN: 10554

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

European-Non Finnish (NFE) AF: 0.391 AC: 26573 AN: 67978

Other (OTH) AF: 0.410 AC: 865 AN: 2108

Alfa AF: 0.389 Hom.: 50423

Bravo AF: 0.362

Asia WGS AF: 0.425 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0060
DANN	Benign	0.29
PhyloP100		-2.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6441286;

hg19: chr3-159728878;