rs1800872
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_153758(IL19):c.-149+1984T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 151940 control chromosomes in the gnomAD Genomes database, including 36691 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.69 ( 36691 hom., cov: 31)
Consequence
IL19
NM_153758 intron
NM_153758 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.260
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 1:206773062-T>G is Benign according to our data. Variant chr1-206773062-T-G is described in ClinVar as [Benign]. Clinvar id is 16873. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL19 | NM_153758.5 | c.-149+1984T>G | intron_variant | ENST00000659997.3 | |||
IL19 | NM_001393490.1 | c.-149+2232T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL19 | ENST00000659997.3 | c.-149+1984T>G | intron_variant | NM_153758.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.686 AC: 104271AN: 151940Hom.: 36691 Cov.: 31
GnomAD3 genomes
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104271
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151940
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31
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1701
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:2Other:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Graft-versus-host disease, resistance to Benign:1
protective, no assertion criteria provided | literature only | OMIM | Dec 04, 2003 | - - |
Inflammatory bowel disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | - - |
Susceptibility to HIV infection Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Dec 04, 2003 | - - |
Cholangiocarcinoma Other:1
other, no assertion criteria provided | research | Department of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin Berlin | Dec 10, 2022 | No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival |
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