chr4-1058337-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001366919.1(RNF212):c.631A>G(p.Met211Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 142,288 control chromosomes in the GnomAD database, including 49,395 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.82 ( 49395 hom., cov: 28)
Exomes 𝑓: 0.68 ( 74337 hom. )
Failed GnomAD Quality Control
Consequence
RNF212
NM_001366919.1 missense
NM_001366919.1 missense
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.80
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
?
Variant 4-1058337-T-C is Benign according to our data. Variant chr4-1058337-T-C is described in ClinVar as [Benign]. Clinvar id is 3046854.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF212 | NM_001366919.1 | c.631A>G | p.Met211Val | missense_variant | 10/12 | ||
RNF212 | NM_001366918.1 | c.631A>G | p.Met211Val | missense_variant | 10/11 | ||
RNF212 | XM_047450083.1 | c.529A>G | p.Met177Val | missense_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF212 | ENST00000698262.1 | c.631A>G | p.Met211Val | missense_variant | 10/12 | P2 | |||
RNF212 | ENST00000503206.5 | n.204A>G | non_coding_transcript_exon_variant | 4/5 | 3 | ||||
RNF212 | ENST00000505693.5 | n.558A>G | non_coding_transcript_exon_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.824 AC: 117218AN: 142172Hom.: 49357 Cov.: 28
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.681 AC: 204917AN: 300886Hom.: 74337 Cov.: 0 AF XY: 0.680 AC XY: 94606AN XY: 139186
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.824 AC: 117308AN: 142288Hom.: 49395 Cov.: 28 AF XY: 0.820 AC XY: 56790AN XY: 69250
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
RNF212-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 07, 2022 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at