rs16924241
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_033439.4(IL33):āc.789C>Gā(p.Ile263Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00193 in 1,613,056 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_033439.4 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 |
---|---|---|---|---|---|---|---|
IL33 | NM_033439.4 | c.789C>G | p.Ile263Met | missense_variant | 8/8 | ENST00000682010.1 | |
LOC107987046 | XR_001746614.2 | n.153-27849G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL33 | ENST00000682010.1 | c.789C>G | p.Ile263Met | missense_variant | 8/8 | NM_033439.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0105 AC: 1595AN: 152008Hom.: 24 Cov.: 32
GnomAD3 exomes AF: 0.00272 AC: 683AN: 250884Hom.: 16 AF XY: 0.00173 AC XY: 235AN XY: 135590
GnomAD4 exome AF: 0.00104 AC: 1513AN: 1460930Hom.: 32 Cov.: 31 AF XY: 0.000892 AC XY: 648AN XY: 726786
GnomAD4 genome AF: 0.0105 AC: 1595AN: 152126Hom.: 24 Cov.: 32 AF XY: 0.00995 AC XY: 740AN XY: 74370
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at