rs11465744

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_016584.3(IL23A):​c.-35G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,358,458 control chromosomes in the GnomAD database, including 35 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 0.0083 ( 22 hom., cov: 31)
Exomes 𝑓: 0.00085 ( 13 hom. )

Consequence

IL23A
NM_016584.3 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.639
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00835 (1271/152306) while in subpopulation AFR AF= 0.029 (1204/41556). AF 95% confidence interval is 0.0276. There are 22 homozygotes in gnomad4. There are 625 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 22 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL23ANM_016584.3 linkuse as main transcriptc.-35G>A 5_prime_UTR_variant 1/4 ENST00000228534.6 NP_057668.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL23AENST00000228534.6 linkuse as main transcriptc.-35G>A 5_prime_UTR_variant 1/41 NM_016584.3 ENSP00000228534 P1
IL23AENST00000619177.1 linkuse as main transcriptn.108-416G>A intron_variant, non_coding_transcript_variant 2
IL23AENST00000622119.4 linkuse as main transcriptn.101-416G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.00836
AC:
1273
AN:
152188
Hom.:
22
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0291
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00288
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.00525
GnomAD3 exomes
AF:
0.00259
AC:
365
AN:
140962
Hom.:
8
AF XY:
0.00190
AC XY:
143
AN XY:
75192
show subpopulations
Gnomad AFR exome
AF:
0.0280
Gnomad AMR exome
AF:
0.000784
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000176
Gnomad OTH exome
AF:
0.00144
GnomAD4 exome
AF:
0.000846
AC:
1021
AN:
1206152
Hom.:
13
Cov.:
30
AF XY:
0.000800
AC XY:
465
AN XY:
581032
show subpopulations
Gnomad4 AFR exome
AF:
0.0302
Gnomad4 AMR exome
AF:
0.00110
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000555
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000122
Gnomad4 OTH exome
AF:
0.00140
GnomAD4 genome
AF:
0.00835
AC:
1271
AN:
152306
Hom.:
22
Cov.:
31
AF XY:
0.00839
AC XY:
625
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.0290
Gnomad4 AMR
AF:
0.00287
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.00520
Alfa
AF:
0.00688
Hom.:
1
Bravo
AF:
0.00944
Asia WGS
AF:
0.000866
AC:
3
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
3.4
DANN
Benign
0.75

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11465744; hg19: chr12-56732794; API