1-207489567-T-C

Position:

• chr1-207489567-T-C

Variant summary

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

The NM_001006658.3(CR2):​c.*444T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,216 control chromosomes in the GnomAD database, including 58,527 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 0.88 (58526 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: CR2 NM_001006658.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CR2	NM_001006658.3	c.*444T>C		3_prime_UTR_variant	20/20	ENST00000367057.8	NP_001006659.1
CR2	NM_001877.5	c.*444T>C		3_prime_UTR_variant	19/19		NP_001868.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CR2	ENST00000367057.8	c.*444T>C		3_prime_UTR_variant	20/20	1	NM_001006658.3	ENSP00000356024.3

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133309 AN: 152096 Hom.: 58489 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.873

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.876 AC: 133401 AN: 152214 Hom.: 58526 Cov.: 32 AF XY: 0.877 AC XY: 65268 AN XY: 74412

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.954

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.873

Alfa AF: 0.872 Hom.: 71987

Bravo AF: 0.878

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.85
DANN	Benign	0.39

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: rs9429940; hg19: chr1-207662912;