chr2-102338283-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_016232.5(IL1RL1):c.19G>T(p.Ala7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000403 in 1,606,812 control chromosomes in the GnomAD database, including 4 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 Likely benign (★).
Frequency
Consequence
NM_016232.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1RL1 | NM_016232.5 | c.19G>T | p.Ala7Ser | missense_variant | 2/11 | ENST00000233954.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RL1 | ENST00000233954.6 | c.19G>T | p.Ala7Ser | missense_variant | 2/11 | 1 | NM_016232.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00130 AC: 197AN: 152098Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00115 AC: 288AN: 249596Hom.: 1 AF XY: 0.000837 AC XY: 113AN XY: 134948
GnomAD4 exome AF: 0.000311 AC: 452AN: 1454596Hom.: 1 Cov.: 27 AF XY: 0.000245 AC XY: 177AN XY: 723818
GnomAD4 genome ? AF: 0.00129 AC: 196AN: 152216Hom.: 3 Cov.: 33 AF XY: 0.00120 AC XY: 89AN XY: 74420
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 22, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at