rs2371494

chr12-56334216-G-Achr12-56334216-G-C

Variant summary

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

The ENST00000619177.1(IL23A):n.9G>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 0.196 in 152,160 control chromosomes in the GnomAD database, including 6,224 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 0.20 (6224 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IL23A ENST00000619177.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

Genes affected

IL23A (HGNC:15488): (interleukin 23 subunit alpha) This gene encodes a subunit of the heterodimeric cytokine interleukin 23 (IL23). IL23 is composed of this protein and the p40 subunit of interleukin 12 (IL12B). The receptor of IL23 is formed by the beta 1 subunit of IL12 (IL12RB1) and an IL23 specific subunit, IL23R. Both IL23 and IL12 can activate the transcription activator STAT4, and stimulate the production of interferon-gamma (IFNG). In contrast to IL12, which acts mainly on naive CD4(+) T cells, IL23 preferentially acts on memory CD4(+) T cells. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL23A	ENST00000619177.1	n.9G>A		non_coding_transcript_exon_variant	1/5	2
IL23A	ENST00000622119.4	n.43G>A		non_coding_transcript_exon_variant	1/5	2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29780 AN: 152042 Hom.: 6192 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.0537

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.127

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.196 AC: 29875 AN: 152160 Hom.: 6224 Cov.: 32 AF XY: 0.190 AC XY: 14124 AN XY: 74398

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0423

Gnomad4 EAS AF: 0.0345

Gnomad4 SAS AF: 0.0209

Gnomad4 FIN AF: 0.0537

Gnomad4 NFE AF: 0.0709

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0754 Hom.: 958

Bravo AF: 0.214

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	3.3
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2371494; hg19: chr12-56728000;