1-145789475-G-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_014455.4(RNF115):c.103-509C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 29)
Failed GnomAD Quality Control
Consequence
RNF115
NM_014455.4 intron
NM_014455.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.62
Genes affected
RNF115 (HGNC:18154): (ring finger protein 115) Enables ubiquitin-protein transferase activity. Involved in negative regulation of epidermal growth factor receptor signaling pathway; protein autoubiquitination; and ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF115 | NM_014455.4 | c.103-509C>A | intron_variant | ENST00000582693.5 | |||
RNF115 | XM_047418024.1 | c.-49-509C>A | intron_variant | ||||
RNF115 | XM_047418027.1 | c.-82-4879C>A | intron_variant | ||||
RNF115 | XM_047418028.1 | c.103-509C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF115 | ENST00000582693.5 | c.103-509C>A | intron_variant | 1 | NM_014455.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 150048Hom.: 0 Cov.: 29 FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 150048Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 73124
GnomAD4 genome
Data not reliable, filtered out with message: AC0
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at