1-185087577-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_007212.4(RNF2):c.24C>T(p.Asn8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,614,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00018 ( 0 hom. )
Consequence
RNF2
NM_007212.4 synonymous
NM_007212.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.09
Genes affected
RNF2 (HGNC:10061): (ring finger protein 2) Polycomb group (PcG) of proteins form the multiprotein complexes that are important for the transcription repression of various genes involved in development and cell proliferation. The protein encoded by this gene is one of the PcG proteins. It has been shown to interact with, and suppress the activity of, transcription factor CP2 (TFCP2/CP2). Studies of the mouse counterpart suggested the involvement of this gene in the specification of anterior-posterior axis, as well as in cell proliferation in early development. This protein was also found to interact with huntingtin interacting protein 2 (HIP2), an ubiquitin-conjugating enzyme, and possess ubiquitin ligase activity. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 1-185087577-C-T is Benign according to our data. Variant chr1-185087577-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2639639.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.09 with no splicing effect.
BS2
High AC in GnomAd4 at 31 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF2 | NM_007212.4 | c.24C>T | p.Asn8= | synonymous_variant | 2/7 | ENST00000367510.8 | |
RNF2 | XM_011509851.4 | c.24C>T | p.Asn8= | synonymous_variant | 2/7 | ||
RNF2 | XM_011509852.3 | c.24C>T | p.Asn8= | synonymous_variant | 2/7 | ||
RNF2 | XM_005245413.4 | c.-138C>T | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF2 | ENST00000367510.8 | c.24C>T | p.Asn8= | synonymous_variant | 2/7 | 1 | NM_007212.4 | P1 | |
RNF2 | ENST00000367509.8 | c.24C>T | p.Asn8= | synonymous_variant | 2/6 | 2 | |||
RNF2 | ENST00000453650.2 | c.24C>T | p.Asn8= | synonymous_variant | 2/5 | 5 | |||
RNF2 | ENST00000498201.1 | n.140C>T | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152154Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000175 AC: 44AN: 251352Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135842
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GnomAD4 exome AF: 0.000183 AC: 267AN: 1461764Hom.: 0 Cov.: 30 AF XY: 0.000164 AC XY: 119AN XY: 727188
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GnomAD4 genome AF: 0.000204 AC: 31AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74464
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | RNF2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at