X-28789354-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_014271.4(IL1RAPL1):c.11C>T(p.Pro4Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000937 in 1,205,768 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 40 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P4P) has been classified as Likely benign.
Frequency
Consequence
NM_014271.4 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 |
---|---|---|---|---|---|---|---|
IL1RAPL1 | NM_014271.4 | c.11C>T | p.Pro4Leu | missense_variant | 2/11 | ENST00000378993.6 | |
IL1RAPL1 | XM_017029240.2 | c.11C>T | p.Pro4Leu | missense_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RAPL1 | ENST00000378993.6 | c.11C>T | p.Pro4Leu | missense_variant | 2/11 | 1 | NM_014271.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000537 AC: 6AN: 111740Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33930
GnomAD3 exomes AF: 0.0000764 AC: 14AN: 183259Hom.: 0 AF XY: 0.000103 AC XY: 7AN XY: 67735
GnomAD4 exome AF: 0.0000978 AC: 107AN: 1094028Hom.: 0 Cov.: 28 AF XY: 0.000111 AC XY: 40AN XY: 359668
GnomAD4 genome AF: 0.0000537 AC: 6AN: 111740Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33930
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 20, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | IL1RAPL1: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at