Variant rs60035268 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001131034.4(RNF212):c.247-2861C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,536,132 control chromosomes in the GnomAD database, including 21,129 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1346 hom., cov: 33)

Exomes 𝑓: 0.16 ( 19783 hom. )

Consequence

RNF212
NM_001131034.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.362

Variant links:

Genes affected

RNF212 (HGNC:27729): (ring finger protein 212) This gene encodes a RING finger protein that may function as a ubiquitin ligase. The encoded protein may be involved in meiotic recombination. This gene is located within a linkage disequilibrium block and polymorphisms in this gene may influence recombination rates. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2010]

RNF212 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_addAF=-0.879525).

BP6

Variant 4-1093699-G-A is Benign according to our data. Variant chr4-1093699-G-A is described in ClinVar as [Benign]. Clinvar id is 403382.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF212	NM_001131034.4 linkuse as main transcript	c.247-2861C>T		intron_variant		ENST00000433731.7	NP_001124506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF212	ENST00000433731.7 linkuse as main transcript	c.247-2861C>T		intron_variant		1	NM_001131034.4	ENSP00000389709	A2	Q495C1-1

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17496

AN:

152164

Hom.:

1347

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0311

Gnomad AMI

AF:

0.166

Gnomad AMR

AF:

0.0982

Gnomad ASJ

AF:

0.0738

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.0465

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.0948

GnomAD3 exomes

AF:

0.109

AC:

14884

AN:

136428

Hom.:

1149

AF XY:

0.109

AC XY:

8076

AN XY:

74170

show subpopulations

Gnomad AFR exome

AF:

0.0290

Gnomad AMR exome

AF:

0.0834

Gnomad ASJ exome

AF:

0.0692

Gnomad EAS exome

AF:

0.000190

Gnomad SAS exome

AF:

0.0482

Gnomad FIN exome

AF:

0.173

Gnomad NFE exome

AF:

0.176

Gnomad OTH exome

AF:

0.109

GnomAD4 exome

AF:

0.160

AC:

220963

AN:

1383850

Hom.:

19783

Cov.:

AF XY:

0.157

AC XY:

106884

AN XY:

682870

show subpopulations

Gnomad4 AFR exome

AF:

0.0245

Gnomad4 AMR exome

AF:

0.0852

Gnomad4 ASJ exome

AF:

0.0693

Gnomad4 EAS exome

AF:

0.000224

Gnomad4 SAS exome

AF:

0.0484

Gnomad4 FIN exome

AF:

0.168

Gnomad4 NFE exome

AF:

0.184

Gnomad4 OTH exome

AF:

0.130

GnomAD4 genome

AF:

0.115

AC:

17492

AN:

152282

Hom.:

1346

Cov.:

AF XY:

0.112

AC XY:

8372

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0310

Gnomad4 AMR

AF:

0.0980

Gnomad4 ASJ

AF:

0.0738

Gnomad4 EAS

AF:

0.000964

Gnomad4 SAS

AF:

0.0476

Gnomad4 FIN

AF:

0.165

Gnomad4 NFE

AF:

0.178

Gnomad4 OTH

AF:

0.0938

Alfa

AF:

0.155

Hom.:

2581

Bravo

AF:

0.106

TwinsUK

AF:

0.179

AC:

663

ALSPAC

AF:

0.183

AC:

705

ExAC

AF:

0.0659

AC:

1382

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in 1000Genomes: 150/2178=6.8% -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.88

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.4

DANN

Benign

0.96

Eigen

Benign

-0.57

Eigen_PC

Benign

-0.80

FATHMM_MKL

Benign

0.016

MutationTaster

Benign

0.000011

P;P;P

Vest4

0.015

GERP RS

1.0

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