rs17045328

chr1-207478831-A-Gchr1-207478831-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001006658.3(CR2):c.3089-426A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0365 in 152,176 control chromosomes in the GnomAD database, including 282 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 0.037 (282 hom., cov: 32)
• Consequence: CR2 NM_001006658.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CR2	NM_001006658.3	c.3089-426A>G		intron_variant		ENST00000367057.8
CR2	NM_001877.5	c.2912-426A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CR2	ENST00000367057.8	c.3089-426A>G		intron_variant		1	NM_001006658.3	P1

Frequencies

GnomAD3 genomes AF: 0.0366 AC: 5562 AN: 152058 Hom.: 282 Cov.: 32

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.00951

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.0852

Gnomad FIN AF: 0.0409

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0353

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0365 AC: 5557 AN: 152176 Hom.: 282 Cov.: 32 AF XY: 0.0390 AC XY: 2902 AN XY: 74390

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.00951

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.0842

Gnomad4 FIN AF: 0.0409

Gnomad4 NFE AF: 0.0243

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0277 Hom.: 196

Bravo AF: 0.0351

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	9.1
Dann	Benign	0.89

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

Other links and lift over

dbSNP: rs17045328; hg19: chr1-207652176;