chr2-102342258-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_016232.5(IL1RL1):c.646G>A(p.Ala216Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00381 in 1,611,566 control chromosomes in the GnomAD database, including 22 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 Likely benign (★★).
Frequency
Consequence
NM_016232.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1RL1 | NM_016232.5 | c.646G>A | p.Ala216Thr | missense_variant | 6/11 | ENST00000233954.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RL1 | ENST00000233954.6 | c.646G>A | p.Ala216Thr | missense_variant | 6/11 | 1 | NM_016232.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00297 AC: 452AN: 152034Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00416 AC: 1043AN: 250938Hom.: 5 AF XY: 0.00384 AC XY: 521AN XY: 135678
GnomAD4 exome AF: 0.00390 AC: 5687AN: 1459414Hom.: 21 Cov.: 28 AF XY: 0.00384 AC XY: 2789AN XY: 726176
GnomAD4 genome ? AF: 0.00297 AC: 452AN: 152152Hom.: 1 Cov.: 32 AF XY: 0.00258 AC XY: 192AN XY: 74398
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | IL1RL1: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at