4-1056882-C-CG
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001366919.1(RNF212):c.769dupC(p.Arg257ProfsTer20) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00426 in 985,460 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0034 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0044 ( 3 hom. )
Consequence
RNF212
NM_001366919.1 frameshift
NM_001366919.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.10
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNF212 | NM_001366919.1 | c.769dupC | p.Arg257ProfsTer20 | frameshift_variant | Exon 11 of 12 | NP_001353848.1 | ||
RNF212 | XM_047450083.1 | c.667dupC | p.Arg223ProfsTer20 | frameshift_variant | Exon 9 of 10 | XP_047306039.1 | ||
RNF212 | XM_011513446.2 | c.505dupC | p.Arg169ProfsTer20 | frameshift_variant | Exon 6 of 7 | XP_011511748.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNF212 | ENST00000698262.1 | c.769dupC | p.Arg257ProfsTer20 | frameshift_variant | Exon 11 of 12 | ENSP00000513634.1 | ||||
RNF212 | ENST00000505693.5 | n.696dupC | non_coding_transcript_exon_variant | Exon 5 of 6 | 5 | |||||
RNF212 | ENST00000508633.5 | n.351dupC | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00335 AC: 509AN: 152008Hom.: 2 Cov.: 33
GnomAD3 genomes
AF:
AC:
509
AN:
152008
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00443 AC: 3692AN: 833332Hom.: 3 Cov.: 31 AF XY: 0.00437 AC XY: 1684AN XY: 385050
GnomAD4 exome
AF:
AC:
3692
AN:
833332
Hom.:
Cov.:
31
AF XY:
AC XY:
1684
AN XY:
385050
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00335 AC: 510AN: 152128Hom.: 2 Cov.: 33 AF XY: 0.00312 AC XY: 232AN XY: 74384
GnomAD4 genome
AF:
AC:
510
AN:
152128
Hom.:
Cov.:
33
AF XY:
AC XY:
232
AN XY:
74384
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spermatogenic failure 62 Uncertain:1
Oct 10, 2023
Department of Pathology and Laboratory Medicine, Sinai Health System
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: research
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at