rs12118043

Positions:

• chr1-161677034-C-A

Variant summary

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

The ENST00000358671.10(FCGR2B):​c.818-294C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 461,422 control chromosomes in the GnomAD database, including 6,104 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 0.13 (1770 hom., cov: 31)
  • Exomes 𝑓: 0.15 (4334 hom.)
• Consequence: FCGR2B ENST00000358671.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

Genes affected

FCGR2B (HGNC:3618): (Fc gamma receptor IIb) The protein encoded by this gene is a low affinity receptor for the Fc region of immunoglobulin gamma complexes. The encoded protein is involved in the phagocytosis of immune complexes and in the regulation of antibody production by B-cells. Variations in this gene may increase susceptibilty to systemic lupus erythematosus (SLE). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCGR2B	NM_001394477.1	c.818-294C>A		intron_variant		ENST00000358671.10	NP_001381406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCGR2B	ENST00000358671.10	c.818-294C>A		intron_variant		1	NM_001394477.1	ENSP00000351497	P4
FCGR2B	ENST00000236937.13	c.761-294C>A		intron_variant		1		ENSP00000236937	A2
FCGR2B	ENST00000367961.8	c.797-294C>A		intron_variant		1		ENSP00000356938	A2
FCGR2B	ENST00000480308.5	n.3771C>A		non_coding_transcript_exon_variant	5/6	1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20087 AN: 152014 Hom.: 1770 Cov.: 31

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.0996

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.153 AC: 47459 AN: 309290 Hom.: 4334 Cov.: 0 AF XY: 0.149 AC XY: 24165 AN XY: 162064

Gnomad4 AFR exome AF: 0.0358

Gnomad4 AMR exome AF: 0.0892

Gnomad4 ASJ exome AF: 0.0917

Gnomad4 EAS exome AF: 0.0441

Gnomad4 SAS exome AF: 0.103

Gnomad4 FIN exome AF: 0.177

Gnomad4 NFE exome AF: 0.180

Gnomad4 OTH exome AF: 0.152

GnomAD4 genome AF: 0.132 AC: 20079 AN: 152132 Hom.: 1770 Cov.: 31 AF XY: 0.128 AC XY: 9505 AN XY: 74372

Gnomad4 AFR AF: 0.0357

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0561

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.143

Alfa AF: 0.174 Hom.: 3382

Bravo AF: 0.124

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.2
DANN	Benign	0.88

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: rs12118043; hg19: chr1-161646824;