chr1-161677757-T-G

Variant names:

• chr1-161677757-T-G
• rs1050519
• ENST00000480308.5:n.4384T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000480308.5(FCGR2B):​n.4384T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000251 in 398,586 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000025 (0 hom.)
• Consequence: FCGR2B ENST00000480308.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 2 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: Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000480308.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCGR2B	NM_001394477.1	MANE Select	c.*204T>G		3_prime_UTR	Exon 8 of 8	NP_001381406.1
	FCGR2B	NR_169827.1		n.1366T>G		non_coding_transcript_exon	Exon 10 of 10
	FCGR2B	NM_004001.5		c.*204T>G		3_prime_UTR	Exon 9 of 9	NP_003992.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCGR2B	ENST00000480308.5	TSL:1	n.4384T>G		non_coding_transcript_exon	Exon 6 of 6
	FCGR2B	ENST00000358671.10	TSL:1 MANE Select	c.*204T>G		3_prime_UTR	Exon 8 of 8	ENSP00000351497.5
	FCGR2B	ENST00000367961.8	TSL:1	c.*204T>G		3_prime_UTR	Exon 7 of 7	ENSP00000356938.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000251 AC: 1 AN: 398586 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 207764

African (AFR) AF: 0.00 AC: 0 AN: 10876

American (AMR) AF: 0.00 AC: 0 AN: 12816

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12912

East Asian (EAS) AF: 0.00 AC: 0 AN: 27842

South Asian (SAS) AF: 0.00 AC: 0 AN: 33500

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28848

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1828

European-Non Finnish (NFE) AF: 0.00000406 AC: 1 AN: 246286

Other (OTH) AF: 0.00 AC: 0 AN: 23678

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		-0.34

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

Other links and lift over

dbSNP: rs1050519; hg19: chr1-161647547;