1-185100256-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_007212.4(RNF2):c.966C>T(p.Asn322=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000293 in 1,612,394 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 Benign (★).
Frequency
Genomes: 𝑓 0.0016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 0 hom. )
Consequence
RNF2
NM_007212.4 synonymous
NM_007212.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.77
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 1-185100256-C-T is Benign according to our data. Variant chr1-185100256-C-T is described in ClinVar as [Benign]. Clinvar id is 2639640.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 245 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNF2 | NM_007212.4 | c.966C>T | p.Asn322= | synonymous_variant | 7/7 | ENST00000367510.8 | NP_009143.1 | |
RNF2 | XM_011509851.4 | c.966C>T | p.Asn322= | synonymous_variant | 7/7 | XP_011508153.1 | ||
RNF2 | XM_011509852.3 | c.966C>T | p.Asn322= | synonymous_variant | 7/7 | XP_011508154.1 | ||
RNF2 | XM_005245413.4 | c.819C>T | p.Asn273= | synonymous_variant | 6/6 | XP_005245470.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNF2 | ENST00000367510.8 | c.966C>T | p.Asn322= | synonymous_variant | 7/7 | 1 | NM_007212.4 | ENSP00000356480 | P1 | |
RNF2 | ENST00000367509.8 | c.750C>T | p.Asn250= | synonymous_variant | 6/6 | 2 | ENSP00000356479 |
Frequencies
GnomAD3 genomes AF: 0.00161 AC: 245AN: 152034Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000395 AC: 99AN: 250376Hom.: 0 AF XY: 0.000340 AC XY: 46AN XY: 135320
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GnomAD4 exome AF: 0.000155 AC: 227AN: 1460242Hom.: 0 Cov.: 30 AF XY: 0.000136 AC XY: 99AN XY: 726330
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GnomAD4 genome AF: 0.00161 AC: 245AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.00156 AC XY: 116AN XY: 74402
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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 | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | RNF2: BS1, BS2 - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at