1-207466350-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001006658.3(CR2):c.59-176C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,062 control chromosomes in the GnomAD database, including 34,068 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.66 (34068 hom., cov: 32)
• Consequence: CR2 NM_001006658.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.83

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 1-207466350-C-G is Benign according to our data. Variant chr1-207466350-C-G is described in ClinVar as [Benign]. Clinvar id is 1226449.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CR2	NM_001006658.3	c.59-176C>G		intron_variant		ENST00000367057.8
CR2	NM_001877.5	c.59-176C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CR2	ENST00000367057.8	c.59-176C>G		intron_variant		1	NM_001006658.3	P1

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100320 AN: 151944 Hom.: 34063 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.660 AC: 100357 AN: 152062 Hom.: 34068 Cov.: 32 AF XY: 0.668 AC XY: 49668 AN XY: 74302

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.676

Alfa AF: 0.588 Hom.: 1849

Bravo AF: 0.651

Asia WGS AF: 0.805 AC: 2802 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	-0.90
Cadd	Benign	5.1
Dann	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs311311; hg19: chr1-207639695;