Variant rs17258996 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_001006658.3(CR2):c.3188+46T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 1,393,920 control chromosomes in the GnomAD database, including 26,069 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1976 hom., cov: 32)

Exomes 𝑓: 0.19 ( 24093 hom. )

Consequence

CR2
NM_001006658.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0200

Variant links:

Genes affected

CR2 (HGNC:2336): (complement C3d receptor 2) This gene encodes a membrane protein, which functions as a receptor for Epstein-Barr virus (EBV) binding on B and T lymphocytes. Genetic variations in this gene are associated with susceptibility to systemic lupus erythematosus type 9 (SLEB9). Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

CR2 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_noAF=-0.86).

BP6

Variant 1-207480099-T-A is Benign according to our data. Variant chr1-207480099-T-A is described in ClinVar as [Benign]. Clinvar id is 1244973.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CR2	NM_001006658.3 linkuse as main transcript	c.3188+46T>A		intron_variant		ENST00000367057.8	NP_001006659.1	P20023-3
CR2	NM_001877.5 linkuse as main transcript	c.3011+46T>A		intron_variant			NP_001868.2	P20023-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CR2	ENST00000367057.8 linkuse as main transcript	c.3188+46T>A		intron_variant		1	NM_001006658.3	ENSP00000356024.3		P20023-3

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23398

AN:

152068

Hom.:

1976

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0752

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.164

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.181

GnomAD3 exomes

AF:

0.167

AC:

41639

AN:

248916

Hom.:

3702

AF XY:

0.172

AC XY:

23149

AN XY:

134556

show subpopulations

Gnomad AFR exome

AF:

0.0732

Gnomad AMR exome

AF:

0.111

Gnomad ASJ exome

AF:

0.211

Gnomad EAS exome

AF:

0.112

Gnomad SAS exome

AF:

0.164

Gnomad FIN exome

AF:

0.167

Gnomad NFE exome

AF:

0.203

Gnomad OTH exome

AF:

0.195

GnomAD4 exome

AF:

0.193

AC:

239969

AN:

1241734

Hom.:

24093

Cov.:

AF XY:

0.193

AC XY:

121551

AN XY:

629082

show subpopulations

Gnomad4 AFR exome

AF:

0.0732

Gnomad4 AMR exome

AF:

0.117

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.121

Gnomad4 SAS exome

AF:

0.165

Gnomad4 FIN exome

AF:

0.163

Gnomad4 NFE exome

AF:

0.207

Gnomad4 OTH exome

AF:

0.189

GnomAD4 genome

AF:

0.154

AC:

23400

AN:

152186

Hom.:

1976

Cov.:

AF XY:

0.151

AC XY:

11265

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0750

Gnomad4 AMR

AF:

0.141

Gnomad4 ASJ

AF:

0.213

Gnomad4 EAS

AF:

0.106

Gnomad4 SAS

AF:

0.166

Gnomad4 FIN

AF:

0.167

Gnomad4 NFE

AF:

0.201

Gnomad4 OTH

AF:

0.179

Alfa

AF:

0.182

Hom.:

483

Bravo

AF:

0.150

Asia WGS

AF:

0.124

AC:

432

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.6

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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