1-185100256-C-T

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.77
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]

Genome browser will be placed here

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
RNF2NM_007212.4 linkuse as main transcriptc.966C>T p.Asn322= synonymous_variant 7/7 ENST00000367510.8 NP_009143.1
RNF2XM_011509851.4 linkuse as main transcriptc.966C>T p.Asn322= synonymous_variant 7/7 XP_011508153.1
RNF2XM_011509852.3 linkuse as main transcriptc.966C>T p.Asn322= synonymous_variant 7/7 XP_011508154.1
RNF2XM_005245413.4 linkuse as main transcriptc.819C>T p.Asn273= synonymous_variant 6/6 XP_005245470.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RNF2ENST00000367510.8 linkuse as main transcriptc.966C>T p.Asn322= synonymous_variant 7/71 NM_007212.4 ENSP00000356480 P1Q99496-1
RNF2ENST00000367509.8 linkuse as main transcriptc.750C>T p.Asn250= synonymous_variant 6/62 ENSP00000356479 Q99496-2

Frequencies

GnomAD3 genomes
AF:
0.00161
AC:
245
AN:
152034
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00568
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
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:
0.0000294
Gnomad OTH
AF:
0.00192
GnomAD3 exomes
AF:
0.000395
AC:
99
AN:
250376
Hom.:
0
AF XY:
0.000340
AC XY:
46
AN XY:
135320
show subpopulations
Gnomad AFR exome
AF:
0.00550
Gnomad AMR exome
AF:
0.000204
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000330
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000176
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000155
AC:
227
AN:
1460242
Hom.:
0
Cov.:
30
AF XY:
0.000136
AC XY:
99
AN XY:
726330
show subpopulations
Gnomad4 AFR exome
AF:
0.00575
Gnomad4 AMR exome
AF:
0.000202
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000117
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000720
Gnomad4 OTH exome
AF:
0.000265
GnomAD4 genome
AF:
0.00161
AC:
245
AN:
152152
Hom.:
0
Cov.:
32
AF XY:
0.00156
AC XY:
116
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.00566
Gnomad4 AMR
AF:
0.000262
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00190
Alfa
AF:
0.00117
Hom.:
0
Bravo
AF:
0.00168
Asia WGS
AF:
0.000289
AC:
1
AN:
3476
EpiCase
AF:
0.00
EpiControl
AF:
0.0000594

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2022RNF2: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
CADD
Benign
6.5
DANN
Benign
0.57

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: rs148949992; hg19: chr1-185069388; API