chr2-102445316-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001393487.1(IL18RAP):c.1048G>A(p.Val350Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00079 in 1,614,122 control chromosomes in the GnomAD database, including 11 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001393487.1 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 |
---|---|---|---|---|---|---|---|
IL18RAP | NM_001393487.1 | c.1048G>A | p.Val350Ile | missense_variant | 7/10 | ENST00000687160.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL18RAP | ENST00000687160.1 | c.1048G>A | p.Val350Ile | missense_variant | 7/10 | NM_001393487.1 | P1 | ||
IL18RAP | ENST00000264260.6 | c.1048G>A | p.Val350Ile | missense_variant | 9/12 | 1 | P1 | ||
IL18RAP | ENST00000409369.1 | c.622G>A | p.Val208Ile | missense_variant | 7/10 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00375 AC: 571AN: 152182Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00112 AC: 282AN: 251330Hom.: 0 AF XY: 0.000795 AC XY: 108AN XY: 135850
GnomAD4 exome AF: 0.000482 AC: 704AN: 1461822Hom.: 3 Cov.: 31 AF XY: 0.000375 AC XY: 273AN XY: 727206
GnomAD4 genome ? AF: 0.00375 AC: 571AN: 152300Hom.: 8 Cov.: 33 AF XY: 0.00375 AC XY: 279AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 26, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at