rs2276384
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018320.5(RNF121):c.507-120G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.958 in 1,289,150 control chromosomes in the GnomAD database, including 593,369 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 0.92 ( 65287 hom., cov: 33)
Exomes 𝑓: 0.96 ( 528082 hom. )
Consequence
RNF121
NM_018320.5 intron
NM_018320.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.165
Genes affected
RNF121 (HGNC:21070): (ring finger protein 121) The protein encoded by this gene contains a RING finger, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. Several alternatively spliced transcript variants have been noted for this gene, however, not all are likely to encode viable protein products. [provided by RefSeq, Sep 2008]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF121 | NM_018320.5 | c.507-120G>A | intron_variant | ENST00000361756.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF121 | ENST00000361756.8 | c.507-120G>A | intron_variant | 1 | NM_018320.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.924 AC: 140639AN: 152178Hom.: 65253 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.963 AC: 1094804AN: 1136854Hom.: 528082 AF XY: 0.961 AC XY: 546592AN XY: 568492
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GnomAD4 genome ? AF: 0.924 AC: 140730AN: 152296Hom.: 65287 Cov.: 33 AF XY: 0.920 AC XY: 68518AN XY: 74482
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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