3-159998234-A-T

Position:

• chr3-159998234-A-T

Variant summary

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

The ENST00000462431.1(IL12A-AS1):​n.928T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,982 control chromosomes in the GnomAD database, including 14,893 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 0.43 (14893 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: IL12A-AS1 ENST00000462431.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

Genes affected

IL12A-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.823-129T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000462431.1	n.928T>A		non_coding_transcript_exon_variant	5/5	5
IL12A-AS1	ENST00000660728.1	n.299T>A		non_coding_transcript_exon_variant	3/3
IL12A-AS1	ENST00000662594.1	n.562T>A		non_coding_transcript_exon_variant	4/7

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65428 AN: 151864 Hom.: 14875 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.410

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.431 AC: 65490 AN: 151982 Hom.: 14893 Cov.: 31 AF XY: 0.422 AC XY: 31371 AN XY: 74280

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.407

Alfa AF: 0.427 Hom.: 1986

Bravo AF: 0.445

Asia WGS AF: 0.232 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243151; hg19: chr3-159716021;