rs12979860
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong
The ENST00000634967(IFNL4):c.152-152G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 152076 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 0.000013 ( 0 hom., cov: 33)
Consequence
IFNL4
ENST00000634967 intron
ENST00000634967 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.79
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 = 0.0000132 (2/152076) while in subpopulation AFR AF= 0.0000483 (2/41414). AF 95% confidence interval is 0.000008. There are 0 homozygotes in gnomad. There are 1 alleles in male gnomad subpopulation. Median coverage is 33. This position pass quality control queck.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNL4 | NR_074079.1 | n.429-152G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNL4 | ENST00000606380.2 | c.152-152G>C | intron_variant | 1 | A2 | ||||
IFNL4 | ENST00000634680.1 | c.151+282G>C | intron_variant | 1 | A2 | ||||
IFNL4 | ENST00000634967.1 | c.152-152G>C | intron_variant | 1 | P5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152076Hom.: 0 Cov.: 33
GnomAD3 genomes
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Cov.:
33
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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 detailed SpliceAI scores and Pangolin per-transcript scores at