rs1800925
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong
The ENST00000435042(TH2LCRR):n.94+7062G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152002 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. 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: 𝑓 0.0000066 ( 0 hom., cov: 32)
Consequence
TH2LCRR
ENST00000435042 intron, non_coding_transcript
ENST00000435042 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.487
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, gnomad allele frequency = 0.00000658 (1/152002) while in subpopulation NFE AF= 0.0000147 (1/68006). AF 95% confidence interval is 0. There are 0 homozygotes in gnomad. There are 0 alleles in male gnomad subpopulation. Median coverage is 32. This position pass quality control queck.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL13 | NM_001354992.2 | c.-220C>G | 5_prime_UTR_variant | 2/6 | |||
IL13 | NM_001354993.2 | c.-149C>G | 5_prime_UTR_variant | 2/5 | |||
IL13 | NM_001354991.2 | c.-93+487C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TH2LCRR | ENST00000435042.1 | n.94+7062G>C | intron_variant, non_coding_transcript_variant | 5 | |||||
IL13 | ENST00000468334.5 | n.420C>G | non_coding_transcript_exon_variant | 2/5 | 3 | ||||
IL13 | ENST00000487267.5 | n.147C>G | non_coding_transcript_exon_variant | 2/6 | 3 | ||||
IL13 | ENST00000459878.5 | n.107+487C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152002Hom.: 0 Cov.: 32
GnomAD3 genomes
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1
AN:
152002
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Cov.:
32
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at