rs6656401

Positions:

• chr1-207518704-A-G
• chr1-207518704-A-T

Variant summary

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

The NM_000651.6(CR1):​c.488-4907A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,188 control chromosomes in the GnomAD database, including 58,029 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 0.87 (58029 hom., cov: 31)
• Consequence: CR1 NM_000651.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.40

Genes affected

CR1 (HGNC:2334): (complement C3b/C4b receptor 1 (Knops blood group)) This gene is a member of the receptors of complement activation (RCA) family and is located in the 'cluster RCA' region of chromosome 1. The genome is polymorphic at this locus with allele-specific splice variants encoding different isoforms, based on the presence/absence of long homologous repeats (LHRs). The gene encodes a monomeric single-pass type I membrane glycoprotein found on erythrocytes, leukocytes, glomerular podocytes, and splenic follicular dendritic cells. The Knops blood group system is a system of antigens located on this protein. The protein mediates cellular binding to particles and immune complexes that have activated complement. Decreases in expression of this protein and/or mutations in this gene have been associated with gallbladder carcinomas, mesangiocapillary glomerulonephritis, systemic lupus erythematosus, sarcoidosis and Alzheimer's disease. Mutations in this gene have also been associated with a reduction in Plasmodium falciparum rosetting, conferring protection against severe malaria. [provided by RefSeq, May 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CR1	NM_000651.6	c.488-4907A>G		intron_variant		ENST00000367049.9	NP_000642.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CR1	ENST00000367049.9	c.488-4907A>G		intron_variant		5	NM_000651.6	ENSP00000356016	P1

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132269 AN: 152070 Hom.: 57970 Cov.: 31

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.870 AC: 132387 AN: 152188 Hom.: 58029 Cov.: 31 AF XY: 0.872 AC XY: 64857 AN XY: 74380

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.867

Alfa AF: 0.821 Hom.: 47228

Bravo AF: 0.880

Asia WGS AF: 0.933 AC: 3242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.19

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: rs6656401; hg19: chr1-207692049;