chr3-190656441-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000317757.8(IL1RAP):c.1898A>G(p.Asn633Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00356 in 1,537,200 control chromosomes in the GnomAD database, including 187 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000317757.8 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 |
---|---|---|---|---|---|---|---|
IL1RAP | NM_001167931.2 | c.1898A>G | p.Asn633Ser | missense_variant | 12/12 | ||
IL1RAP | NM_001364879.1 | c.1898A>G | p.Asn633Ser | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RAP | ENST00000317757.8 | c.1898A>G | p.Asn633Ser | missense_variant | 12/12 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0186 AC: 2829AN: 152128Hom.: 95 Cov.: 32
GnomAD3 exomes AF: 0.00391 AC: 555AN: 141856Hom.: 14 AF XY: 0.00312 AC XY: 237AN XY: 75962
GnomAD4 exome AF: 0.00188 AC: 2602AN: 1384954Hom.: 87 Cov.: 32 AF XY: 0.00163 AC XY: 1115AN XY: 683398
GnomAD4 genome ? AF: 0.0188 AC: 2868AN: 152246Hom.: 100 Cov.: 32 AF XY: 0.0187 AC XY: 1389AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 18, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at