3-159978311-G-T

Variant names:

• chr3-159978311-G-T
• rs2366408
• ENST00000497452.5:n.1350+10786C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000497452.5(IL12A-AS1):​n.1350+10786C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,480 control chromosomes in the GnomAD database, including 10,066 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 (10066 hom., cov: 31)
• Consequence: IL12A-AS1 ENST00000497452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.1350+10786C>A		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1350+10786C>A		intron_variant	Intron 9 of 9	2
IL12A-AS1	ENST00000642756.1	n.778+10786C>A		intron_variant	Intron 4 of 4
IL12A-AS1	ENST00000654530.1	n.837+10786C>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54175 AN: 151364 Hom.: 10037 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.358 AC: 54264 AN: 151480 Hom.: 10066 Cov.: 31 AF XY: 0.352 AC XY: 26082 AN XY: 73992

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.382

Alfa AF: 0.340 Hom.: 13588

Bravo AF: 0.367

Asia WGS AF: 0.188 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.43
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2366408; hg19: chr3-159696099;