Genetic Variant RNF2:p.Asn322Asn (chr1-185100256-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_007212.4(RNF2):c.966C>T(p.Asn322Asn) 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

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]

RNF2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RNF2	NM_007212.4 link	c.966C>T	p.Asn322Asn	synonymous_variant	Exon 7 of 7	ENST00000367510.8	NP_009143.1
RNF2	XM_011509851.4 link	c.966C>T	p.Asn322Asn	synonymous_variant	Exon 7 of 7		XP_011508153.1	Q99496-1
RNF2	XM_011509852.3 link	c.966C>T	p.Asn322Asn	synonymous_variant	Exon 7 of 7		XP_011508154.1	Q99496-1
RNF2	XM_005245413.4 link	c.819C>T	p.Asn273Asn	synonymous_variant	Exon 6 of 6		XP_005245470.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNF2	ENST00000367510.8 link	c.966C>T	p.Asn322Asn	synonymous_variant	Exon 7 of 7	1	NM_007212.4	ENSP00000356480.3		Q99496-1
RNF2	ENST00000367509.8 link	c.750C>T	p.Asn250Asn	synonymous_variant	Exon 6 of 6	2		ENSP00000356479.4		Q99496-2

Frequencies

GnomAD3 genomes

AF:

0.00161

AC:

245

AN:

152034

Hom.:

Cov.:

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

GnomAD2 exomes

AF:

0.000395

AC:

AN:

250376

AF XY:

0.000340

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 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.:

Cov.:

AF XY:

0.000136

AC XY:

AN XY:

726330

show subpopulations

Gnomad4 AFR exome

AF:

0.00575

AC:

192

AN:

33414

Gnomad4 AMR exome

AF:

0.000202

AC:

AN:

44530

Gnomad4 ASJ exome

AF:

0.00

AC:

AN:

26102

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

39602

Gnomad4 SAS exome

AF:

0.0000117

AC:

AN:

85794

Gnomad4 FIN exome

AF:

0.00

AC:

AN:

53376

Gnomad4 NFE exome

AF:

0.00000720

AC:

AN:

1111412

Gnomad4 Remaining exome

AF:

0.000265

AC:

AN:

60310

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00161

AC:

245

AN:

152152

Hom.:

Cov.:

AF XY:

0.00156

AC XY:

116

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.00566

AC:

0.00566238

AN:

0.00566238

Gnomad4 AMR

AF:

0.000262

AC:

0.000261814

AN:

0.000261814

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.00

AC:

AN:

Gnomad4 FIN

AF:

0.00

AC:

AN:

Gnomad4 NFE

AF:

0.0000294

AC:

0.00002941

AN:

0.00002941

Gnomad4 OTH

AF:

0.00190

AC:

0.00189934

AN:

0.00189934

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00117

Hom.:

Bravo

AF:

0.00168

Asia WGS

AF:

0.000289

AC:

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

Jul 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

RNF2: 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

Mutation Taster

=97/3

polymorphism

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over