rs11949052
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000389100.9(RNF180):c.1-91G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0967 in 1,088,848 control chromosomes in the GnomAD database, including 5,858 homozygotes. 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 0.076 ( 636 hom., cov: 32)
Exomes 𝑓: 0.10 ( 5222 hom. )
Consequence
RNF180
ENST00000389100.9 intron
ENST00000389100.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.697
Genes affected
RNF180 (HGNC:27752): (ring finger protein 180) Predicted to enable ubiquitin conjugating enzyme binding activity and ubiquitin protein ligase activity. Predicted to be involved in norepinephrine metabolic process; positive regulation of proteasomal ubiquitin-dependent protein catabolic process; and serotonin metabolic process. Predicted to act upstream of or within several processes, including adult behavior; positive regulation of protein ubiquitination; and protein polyubiquitination. Predicted to be located in nuclear envelope. Predicted to be integral component of membrane. Predicted to be intrinsic component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNF180 | NM_001113561.2 | c.1-91G>A | intron_variant | ENST00000389100.9 | NP_001107033.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNF180 | ENST00000389100.9 | c.1-91G>A | intron_variant | 1 | NM_001113561.2 | ENSP00000373752 | P1 | |||
RNF180 | ENST00000296615.10 | c.1-91G>A | intron_variant | 1 | ENSP00000296615 | |||||
RNF180 | ENST00000504296.1 | c.1-91G>A | intron_variant | 3 | ENSP00000426884 |
Frequencies
GnomAD3 genomes AF: 0.0765 AC: 11634AN: 152098Hom.: 639 Cov.: 32
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GnomAD4 exome AF: 0.100 AC: 93692AN: 936632Hom.: 5222 AF XY: 0.0988 AC XY: 47163AN XY: 477234
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GnomAD4 genome AF: 0.0764 AC: 11627AN: 152216Hom.: 636 Cov.: 32 AF XY: 0.0748 AC XY: 5570AN XY: 74432
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ClinVar
Not reported inComputational scores
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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