chr2-102172706-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000877.4(IL1R1):c.859A>G(p.Lys287Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000873 in 1,604,514 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000877.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1R1 | NM_000877.4 | c.859A>G | p.Lys287Glu | missense_variant | 9/12 | ENST00000410023.6 | |
IL1R1-AS1 | NR_174960.1 | n.306-9T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1R1 | ENST00000410023.6 | c.859A>G | p.Lys287Glu | missense_variant | 9/12 | 1 | NM_000877.4 | P1 | |
IL1R1-AS1 | ENST00000428188.1 | n.306-9T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000166 AC: 4AN: 240986Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 130656
GnomAD4 exome AF: 0.00000689 AC: 10AN: 1452286Hom.: 0 Cov.: 29 AF XY: 0.00000554 AC XY: 4AN XY: 722446
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.859A>G (p.K287E) alteration is located in exon 8 (coding exon 7) of the IL1R1 gene. This alteration results from a A to G substitution at nucleotide position 859, causing the lysine (K) at amino acid position 287 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at