chrX-104658929-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_017416.2(IL1RAPL2):c.16C>T(p.Leu6Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000378 in 1,203,410 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 147 hemizygotes in GnomAD. 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_017416.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1RAPL2 | NM_017416.2 | c.16C>T | p.Leu6Phe | missense_variant | 2/11 | ENST00000372582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RAPL2 | ENST00000372582.6 | c.16C>T | p.Leu6Phe | missense_variant | 2/11 | 1 | NM_017416.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000403 AC: 45AN: 111766Hom.: 0 Cov.: 24 AF XY: 0.000265 AC XY: 9AN XY: 33978
GnomAD3 exomes AF: 0.000337 AC: 60AN: 178003Hom.: 0 AF XY: 0.000397 AC XY: 25AN XY: 62965
GnomAD4 exome AF: 0.000376 AC: 410AN: 1091644Hom.: 0 Cov.: 28 AF XY: 0.000386 AC XY: 138AN XY: 357704
GnomAD4 genome ? AF: 0.000403 AC: 45AN: 111766Hom.: 0 Cov.: 24 AF XY: 0.000265 AC XY: 9AN XY: 33978
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.16C>T (p.L6F) alteration is located in exon 2 (coding exon 1) of the IL1RAPL2 gene. This alteration results from a C to T substitution at nucleotide position 16, causing the leucine (L) at amino acid position 6 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | IL1RAPL2: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at