rs1670533
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001131034.4(RNF212):c.362+1497C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,092 control chromosomes in the GnomAD database, including 50,705 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.81 ( 50705 hom., cov: 31)
Consequence
RNF212
NM_001131034.4 intron
NM_001131034.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.31
Genes affected
RNF212 (HGNC:27729): (ring finger protein 212) This gene encodes a RING finger protein that may function as a ubiquitin ligase. The encoded protein may be involved in meiotic recombination. This gene is located within a linkage disequilibrium block and polymorphisms in this gene may influence recombination rates. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2010]
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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=-1.03).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF212 | NM_001131034.4 | c.362+1497C>T | intron_variant | ENST00000433731.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF212 | ENST00000433731.7 | c.362+1497C>T | intron_variant | 1 | NM_001131034.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.811 AC: 123234AN: 151974Hom.: 50669 Cov.: 31
GnomAD3 genomes
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151974
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.811 AC: 123322AN: 152092Hom.: 50705 Cov.: 31 AF XY: 0.806 AC XY: 59953AN XY: 74356
GnomAD4 genome
?
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123322
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31
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59953
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74356
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2320
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3478
ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Recombination rate quantitative trait locus 1 Other:1
association, no assertion criteria provided | literature only | OMIM | Mar 07, 2008 | - - |
Computational scores
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Name
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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