chr4-1093477-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001131034.4(RNF212):c.247-2639A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 1,449,300 control chromosomes in the GnomAD database, including 440,015 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.81 ( 50998 hom., cov: 32)
Exomes 𝑓: 0.77 ( 389017 hom. )
Consequence
RNF212
NM_001131034.4 intron
NM_001131034.4 intron
Scores
13
Clinical Significance
Conservation
PhyloP100: -3.60
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 (MetaRNN=1.5909047E-6).
BP6
?
Variant 4-1093477-T-C is Benign according to our data. Variant chr4-1093477-T-C is described in ClinVar as [Benign]. Clinvar id is 1222937.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-1093477-T-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF212 | NM_001131034.4 | c.247-2639A>G | intron_variant | ENST00000433731.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF212 | ENST00000433731.7 | c.247-2639A>G | intron_variant | 1 | NM_001131034.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.813 AC: 123568AN: 152022Hom.: 50959 Cov.: 32
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GnomAD3 exomes AF: 0.712 AC: 53742AN: 75470Hom.: 19589 AF XY: 0.707 AC XY: 27981AN XY: 39596
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GnomAD4 exome AF: 0.772 AC: 1001750AN: 1297160Hom.: 389017 Cov.: 38 AF XY: 0.771 AC XY: 486205AN XY: 630502
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GnomAD4 genome ? AF: 0.813 AC: 123660AN: 152140Hom.: 50998 Cov.: 32 AF XY: 0.808 AC XY: 60071AN XY: 74348
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2019 | This variant is associated with the following publications: (PMID: 30679340) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Vest4
ClinPred
T
GERP RS
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