X-28789425-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_014271.4(IL1RAPL1):c.82G>A(p.Ala28Thr) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000145 in 1,175,560 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_014271.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL1RAPL1 | NM_014271.4 | c.82G>A | p.Ala28Thr | missense_variant, splice_region_variant | Exon 2 of 11 | ENST00000378993.6 | NP_055086.1 | |
IL1RAPL1 | XM_017029240.2 | c.82G>A | p.Ala28Thr | missense_variant, splice_region_variant | Exon 2 of 11 | XP_016884729.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000268 AC: 3AN: 111760Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33944
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183295Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67773
GnomAD4 exome AF: 0.0000132 AC: 14AN: 1063800Hom.: 0 Cov.: 26 AF XY: 0.0000210 AC XY: 7AN XY: 332562
GnomAD4 genome AF: 0.0000268 AC: 3AN: 111760Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33944
ClinVar
Submissions by phenotype
Intellectual disability, X-linked 21 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 06, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at