1-67240275-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_144701.3(IL23R):c.1142G>A(p.Arg381Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0548 in 1,604,812 control chromosomes in the GnomAD database, including 2,839 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.046 ( 217 hom., cov: 33)
Exomes 𝑓: 0.056 ( 2622 hom. )
Consequence
IL23R
NM_144701.3 missense
NM_144701.3 missense
Scores
1
4
7
Clinical Significance
Conservation
PhyloP100: 2.74
Genes affected
IL23R (HGNC:19100): (interleukin 23 receptor) The protein encoded by this gene is a subunit of the receptor for IL23A/IL23. This protein pairs with the receptor molecule IL12RB1/IL12Rbeta1, and both are required for IL23A signaling. This protein associates constitutively with Janus kinase 2 (JAK2), and also binds to transcription activator STAT3 in a ligand-dependent manner. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0025800169).
BP6
?
Variant 1-67240275-G-A is Benign according to our data. Variant chr1-67240275-G-A is described in ClinVar as [Benign]. Clinvar id is 3108.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0648 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL23R | NM_144701.3 | c.1142G>A | p.Arg381Gln | missense_variant | 9/11 | ENST00000347310.10 | |
IL23R | XM_011540790.4 | c.1142G>A | p.Arg381Gln | missense_variant | 9/11 | ||
IL23R | XM_011540791.4 | c.1142G>A | p.Arg381Gln | missense_variant | 9/11 | ||
IL23R | XM_047447227.1 | c.1142G>A | p.Arg381Gln | missense_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL23R | ENST00000347310.10 | c.1142G>A | p.Arg381Gln | missense_variant | 9/11 | 1 | NM_144701.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0458 AC: 6971AN: 152044Hom.: 217 Cov.: 33
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GnomAD3 exomes AF: 0.0422 AC: 10589AN: 250900Hom.: 306 AF XY: 0.0426 AC XY: 5771AN XY: 135628
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GnomAD4 exome AF: 0.0558 AC: 80990AN: 1452650Hom.: 2622 Cov.: 28 AF XY: 0.0548 AC XY: 39655AN XY: 723268
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GnomAD4 genome ? AF: 0.0458 AC: 6970AN: 152162Hom.: 217 Cov.: 33 AF XY: 0.0450 AC XY: 3350AN XY: 74384
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234
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272
ESP6500AA
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inflammatory bowel disease 17, protection against Benign:1
protective, no assertion criteria provided | literature only | OMIM | Apr 01, 2010 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Psoriasis, protection against Benign:1
protective, no assertion criteria provided | literature only | OMIM | Apr 01, 2010 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;N
PrimateAI
Benign
T
Polyphen
1.0
.;D;D
Vest4
0.24, 0.17
MPC
0.59
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at