chr3-160011091-T-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.583-1834A>C		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000462431.1	n.698+375A>C		intron_variant	Intron 3 of 4	5
IL12A-AS1	ENST00000497452.5	n.583-1834A>C		intron_variant	Intron 4 of 9	2
IL12A-AS1	ENST00000642756.1	n.367-1834A>C		intron_variant	Intron 1 of 4

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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.410

Alfa AF: 0.396 Hom.: 24577

Bravo AF: 0.362

Asia WGS AF: 0.425 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6441286; hg19: chr3-159728878;