1-161668740-G-A

Variant names:

• chr1-161668740-G-A
• rs2007773
• NM_001394477.1:c.113-1512G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394477.1(FCGR2B):​c.113-1512G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.98 (40583 hom., cov: 11)
• Consequence: FCGR2B NM_001394477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 4 publications found

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]

FCGR2B Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE, NO_KNOWN Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394477.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCGR2B	NM_001394477.1	MANE Select	c.113-1512G>A		intron	N/A	NP_001381406.1	P31994-1
	FCGR2B	NM_004001.5		c.113-1512G>A		intron	N/A	NP_003992.3
	FCGR2B	NM_001002275.3		c.113-1512G>A		intron	N/A	NP_001002275.1	P31994-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCGR2B	ENST00000358671.10	TSL:1 MANE Select	c.113-1512G>A		intron	N/A	ENSP00000351497.5	P31994-1
	FCGR2B	ENST00000367961.8	TSL:1	c.113-2652G>A		intron	N/A	ENSP00000356938.4	P31994-3
	FCGR2B	ENST00000236937.13	TSL:1	c.113-1512G>A		intron	N/A	ENSP00000236937.9	P31994-2

Frequencies

GnomAD3 genomes AF: 0.978 AC: 82326 AN: 84170 Hom.: 40543 Cov.: 11

Gnomad AFR AF: 0.929

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.990

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.970

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.977

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

GnomAD4 genome AF: 0.978 AC: 82406 AN: 84250 Hom.: 40583 Cov.: 11 AF XY: 0.979 AC XY: 39594 AN XY: 40454

African (AFR) AF: 0.929 AC: 20677 AN: 22262

American (AMR) AF: 0.990 AC: 9229 AN: 9322

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 1828 AN: 1828

East Asian (EAS) AF: 1.00 AC: 3980 AN: 3980

South Asian (SAS) AF: 1.00 AC: 2495 AN: 2496

European-Finnish (FIN) AF: 1.00 AC: 5067 AN: 5068

Middle Eastern (MID) AF: 0.969 AC: 124 AN: 128

European-Non Finnish (NFE) AF: 0.996 AC: 37183 AN: 37318

Other (OTH) AF: 0.977 AC: 1057 AN: 1082

Alfa AF: 0.970 Hom.: 5786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.76
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2007773; hg19: chr1-161638530;