ENST00000480308.5:n.4370A>C

Variant names:

• chr1-161677743-A-C
• rs844
• ENST00000480308.5:n.4370A>C

Variant summary

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

The ENST00000480308.5(FCGR2B):​n.4370A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FCGR2B ENST00000480308.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 20 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=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCGR2B	NM_001394477.1	c.*190A>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000358671.10	NP_001381406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCGR2B	ENST00000480308.5	n.4370A>C		non_coding_transcript_exon_variant	Exon 6 of 6	1
FCGR2B	ENST00000358671.10	c.*190A>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_001394477.1	ENSP00000351497.5
FCGR2B	ENST00000367961.8	c.*190A>C		3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000356938.4
FCGR2B	ENST00000236937.13	c.*190A>C		3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000236937.9

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 409004 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 213698

African (AFR) AF: 0.00 AC: 0 AN: 10874

American (AMR) AF: 0.00 AC: 0 AN: 13310

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13062

East Asian (EAS) AF: 0.00 AC: 0 AN: 28128

South Asian (SAS) AF: 0.00 AC: 0 AN: 34714

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30138

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1874

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 252742

Other (OTH) AF: 0.00 AC: 0 AN: 24162

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.61
PhyloP100		0.079

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: rs844; hg19: chr1-161647533;