1-185087577-C-T

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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.09
Variant links:
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
RNF2NM_007212.4 linkuse as main transcriptc.24C>T p.Asn8= synonymous_variant 2/7 ENST00000367510.8
RNF2XM_011509851.4 linkuse as main transcriptc.24C>T p.Asn8= synonymous_variant 2/7
RNF2XM_011509852.3 linkuse as main transcriptc.24C>T p.Asn8= synonymous_variant 2/7
RNF2XM_005245413.4 linkuse as main transcriptc.-138C>T 5_prime_UTR_variant 1/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RNF2ENST00000367510.8 linkuse as main transcriptc.24C>T p.Asn8= synonymous_variant 2/71 NM_007212.4 P1Q99496-1
RNF2ENST00000367509.8 linkuse as main transcriptc.24C>T p.Asn8= synonymous_variant 2/62 Q99496-2
RNF2ENST00000453650.2 linkuse as main transcriptc.24C>T p.Asn8= synonymous_variant 2/55
RNF2ENST00000498201.1 linkuse as main transcriptn.140C>T non_coding_transcript_exon_variant 2/32

Frequencies

GnomAD3 genomes
AF:
0.000204
AC:
31
AN:
152154
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000323
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.000175
AC:
44
AN:
251352
Hom.:
0
AF XY:
0.000169
AC XY:
23
AN XY:
135842
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000318
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000273
Gnomad OTH exome
AF:
0.000326
GnomAD4 exome
AF:
0.000183
AC:
267
AN:
1461764
Hom.:
0
Cov.:
30
AF XY:
0.000164
AC XY:
119
AN XY:
727188
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.000313
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000219
Gnomad4 OTH exome
AF:
0.000116
GnomAD4 genome
AF:
0.000204
AC:
31
AN:
152272
Hom.:
0
Cov.:
32
AF XY:
0.000201
AC XY:
15
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.0000722
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000323
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.000213
Hom.:
0
Bravo
AF:
0.000178
EpiCase
AF:
0.000273
EpiControl
AF:
0.000356

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenAug 01, 2022RNF2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
CADD
Benign
6.9
DANN
Benign
0.63
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201683390; hg19: chr1-185056709; API