rs1800890
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong
The NM_153758(IL19):c.-149+4942A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
IL19
NM_153758 intron
NM_153758 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.103
Links
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL19 | NM_153758.5 | c.-149+4942A>C | intron_variant | ENST00000659997.3 | |||
IL19 | NM_001393490.1 | c.-149+5190A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL19 | ENST00000659997.3 | c.-149+4942A>C | intron_variant | NM_153758.5 | P1 | ||||
IL19 | ENST00000656872.2 | c.-149+5190A>C | intron_variant | P1 | |||||
IL19 | ENST00000662320.1 | n.67+5190A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomesCov.: 32
GnomAD3 genomes
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at