Variant 1-207454573-G-A 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.58+97G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0926 in 953,620 control chromosomes in the GnomAD database, including 4,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.083 ( 563 hom., cov: 32)

Exomes 𝑓: 0.094 ( 4135 hom. )

Consequence

CR2
NM_001006658.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0990

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 1-207454573-G-A is Benign according to our data. Variant chr1-207454573-G-A is described in ClinVar as [Benign]. Clinvar id is 1166837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CR2	NM_001006658.3 link	c.58+97G>A		intron_variant	Intron 1 of 19	ENST00000367057.8	NP_001006659.1	P20023-3
CR2	NM_001877.5 link	c.58+97G>A		intron_variant	Intron 1 of 18		NP_001868.2	P20023-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CR2	ENST00000367057.8 link	c.58+97G>A		intron_variant	Intron 1 of 19	1	NM_001006658.3	ENSP00000356024.3		P20023-3

Frequencies

GnomAD3 genomes

AF:

0.0827

AC:

12586

AN:

152144

Hom.:

563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0770

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.0575

Gnomad ASJ

AF:

0.0467

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0515

Gnomad FIN

AF:

0.0606

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.0678

GnomAD4 exome

AF:

0.0945

AC:

75701

AN:

801358

Hom.:

4135

Cov.:

AF XY:

0.0928

AC XY:

37434

AN XY:

403490

show subpopulations

Gnomad4 AFR exome

AF:

0.0736

Gnomad4 AMR exome

AF:

0.0459

Gnomad4 ASJ exome

AF:

0.0561

Gnomad4 EAS exome

AF:

0.000257

Gnomad4 SAS exome

AF:

0.0562

Gnomad4 FIN exome

AF:

0.0694

Gnomad4 NFE exome

AF:

0.109

Gnomad4 OTH exome

AF:

0.0811

GnomAD4 genome

AF:

0.0827

AC:

12591

AN:

152262

Hom.:

563

Cov.:

AF XY:

0.0798

AC XY:

5943

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0770

Gnomad4 AMR

AF:

0.0573

Gnomad4 ASJ

AF:

0.0467

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0522

Gnomad4 FIN

AF:

0.0606

Gnomad4 NFE

AF:

0.107

Gnomad4 OTH

AF:

0.0676

Alfa

AF:

0.0924

Hom.:

Bravo

AF:

0.0808

Asia WGS

AF:

0.0350

AC:

120

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Immunodeficiency, common variable, 7

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 11, 2023

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 25180293) -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

5.0

DANN

Benign

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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