ENST00000497452.5:n.1003G>A

Variant names:

• chr3-159997925-C-T
• rs2243149
• ENST00000497452.5:n.1003G>A

Variant summary

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

The ENST00000497452.5(IL12A-AS1):​n.1003G>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 151,964 control chromosomes in the GnomAD database, including 14,907 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 (14903 hom., cov: 32)
  • Exomes 𝑓: 0.40 (4 hom.)
• Consequence: IL12A-AS1 ENST00000497452.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1	n.1003G>A		non_coding_transcript_exon_variant	Exon 7 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL12A-AS1	ENST00000497452.5	n.1003G>A		non_coding_transcript_exon_variant	Exon 7 of 10	2
IL12A-AS1	ENST00000654530.1	n.490G>A		non_coding_transcript_exon_variant	Exon 2 of 5
IL12A-AS1	ENST00000656481.1	n.686G>A		non_coding_transcript_exon_variant	Exon 4 of 7

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65449 AN: 151806 Hom.: 14885 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.393

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 AF: 0.400 AC: 16 AN: 40 Hom.: 4 Cov.: 0 AF XY: 0.357 AC XY: 10 AN XY: 28

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.385 AC: 10 AN: 26

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.431 AC: 65511 AN: 151924 Hom.: 14903 Cov.: 32 AF XY: 0.423 AC XY: 31401 AN XY: 74266

African (AFR) AF: 0.577 AC: 23879 AN: 41404

American (AMR) AF: 0.392 AC: 5989 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3468

East Asian (EAS) AF: 0.164 AC: 849 AN: 5176

South Asian (SAS) AF: 0.234 AC: 1125 AN: 4814

European-Finnish (FIN) AF: 0.379 AC: 3996 AN: 10542

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27243 AN: 67940

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.415 Hom.: 4926

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	-0.86
CADD	Benign	0.34
DANN	Benign	0.72
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2243149; hg19: chr3-159715712;