chr4-1058283-AGAACGCAGTGAAGAAGGTGCTTGCGGGGG-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001366919.1(RNF212):c.647+9_647+37del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0461 in 144,794 control chromosomes in the GnomAD database, including 253 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.046 ( 253 hom., cov: 27)
Exomes 𝑓: 0.047 ( 3059 hom. )
Failed GnomAD Quality Control
Consequence
RNF212
NM_001366919.1 intron
NM_001366919.1 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.598
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 -10 ACMG points.
BP6
?
Variant 4-1058283-AGAACGCAGTGAAGAAGGTGCTTGCGGGGG-A is Benign according to our data. Variant chr4-1058283-AGAACGCAGTGAAGAAGGTGCTTGCGGGGG-A is described in ClinVar as [Likely_benign]. Clinvar id is 3033074.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0566 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF212 | NM_001366918.1 | c.647+9_647+37del | intron_variant | ||||
RNF212 | NM_001366919.1 | c.647+9_647+37del | intron_variant | ||||
RNF212 | XM_011513446.2 | c.383+9_383+37del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF212 | ENST00000698262.1 | c.647+9_647+37del | intron_variant | P2 | |||||
RNF212 | ENST00000506730.5 | c.*426+9_*426+37del | intron_variant, NMD_transcript_variant | 3 | |||||
RNF212 | ENST00000503206.5 | n.220+9_220+37del | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0461 AC: 6672AN: 144702Hom.: 253 Cov.: 27
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0471 AC: 27149AN: 576688Hom.: 3059 AF XY: 0.0468 AC XY: 12580AN XY: 268740
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GnomAD4 genome ? AF: 0.0461 AC: 6671AN: 144794Hom.: 253 Cov.: 27 AF XY: 0.0431 AC XY: 3049AN XY: 70684
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
RNF212-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 09, 2023 | This variant is classified as likely 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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Find out detailed SpliceAI scores and Pangolin per-transcript scores at