rs41313262
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_144701.3(IL23R):c.1084G>A(p.Val362Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,612,506 control chromosomes in the GnomAD database, including 171 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_144701.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL23R | NM_144701.3 | c.1084G>A | p.Val362Ile | missense_variant | 9/11 | ENST00000347310.10 | |
IL23R | XM_011540790.4 | c.1084G>A | p.Val362Ile | missense_variant | 9/11 | ||
IL23R | XM_011540791.4 | c.1084G>A | p.Val362Ile | missense_variant | 9/11 | ||
IL23R | XM_047447227.1 | c.1084G>A | p.Val362Ile | missense_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL23R | ENST00000347310.10 | c.1084G>A | p.Val362Ile | missense_variant | 9/11 | 1 | NM_144701.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0100 AC: 1525AN: 152082Hom.: 14 Cov.: 33
GnomAD3 exomes AF: 0.0111 AC: 2778AN: 251222Hom.: 28 AF XY: 0.0116 AC XY: 1572AN XY: 135796
GnomAD4 exome AF: 0.0127 AC: 18492AN: 1460306Hom.: 157 Cov.: 29 AF XY: 0.0125 AC XY: 9080AN XY: 726596
GnomAD4 genome ? AF: 0.0100 AC: 1524AN: 152200Hom.: 14 Cov.: 33 AF XY: 0.00934 AC XY: 695AN XY: 74414
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at