rs1800896
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_153758.5(IL19):c.-149+2474T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 150900 control chromosomes in the gnomAD Genomes database, including 12903 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain risk allele (no stars).
Frequency
Genomes: 𝑓 0.40 ( 12903 hom., cov: 29)
Consequence
IL19
NM_153758.5 intron
NM_153758.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0260
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL19 | NM_153758.5 | c.-149+2474T>C | intron_variant | ENST00000659997.3 | |||
IL19 | NM_001393490.1 | c.-149+2722T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL19 | ENST00000659997.3 | c.-149+2474T>C | intron_variant | NM_153758.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.401 AC: 60462AN: 150900Hom.: 12903 Cov.: 29
GnomAD3 genomes
AF:
AC:
60462
AN:
150900
Hom.:
Cov.:
29
Gnomad AFR
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Asia WGS
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AC:
554
AN:
3478
ClinVar
Significance: Uncertain risk allele
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Leprosy, susceptibility to, 1 Other:1
Uncertain risk allele, no assertion criteria provided | case-control | Centro Dermatológico Federico Lleras Acosta, Hospital Universitario Centro Dermatológico Federico Lleras Acosta | Jun 10, 2022 | - - |
Computational 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