dbSNP rs17045761: CR2:c.*888G>A (chr1-207490011-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001006658.3(CR2):c.*888G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0583 in 151,908 control chromosomes in the GnomAD database, including 317 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.058 ( 317 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CR2
NM_001006658.3 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.267

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CR2	NM_001006658.3 link	c.*888G>A		downstream_gene_variant		ENST00000367057.8	NP_001006659.1	P20023-3
CR2	NM_001877.5 link	c.*888G>A		downstream_gene_variant			NP_001868.2	P20023-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CR2	ENST00000367057.8 link	c.*888G>A		downstream_gene_variant		1	NM_001006658.3	ENSP00000356024.3		P20023-3

Frequencies

GnomAD3 genomes

AF:

0.0584

AC:

8859

AN:

151786

Hom.:

318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0498

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.0666

Gnomad ASJ

AF:

0.0447

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.0927

Gnomad FIN

AF:

0.0675

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0501

Gnomad OTH

AF:

0.0733

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.250

AC:

AN:

Hom.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.00

GnomAD4 genome

AF:

0.0583

AC:

8860

AN:

151908

Hom.:

317

Cov.:

AF XY:

0.0608

AC XY:

4509

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.0496

Gnomad4 AMR

AF:

0.0665

Gnomad4 ASJ

AF:

0.0447

Gnomad4 EAS

AF:

0.151

Gnomad4 SAS

AF:

0.0922

Gnomad4 FIN

AF:

0.0675

Gnomad4 NFE

AF:

0.0501

Gnomad4 OTH

AF:

0.0743

Alfa

AF:

0.0506

Hom.:

Bravo

AF:

0.0581

Asia WGS

AF:

0.0910

AC:

316

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.4

DANN

Benign

0.76

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over