1-161629785-G-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001244753.2(FCGR3B):c.312C>A(p.Val104=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,431,338 control chromosomes in the GnomAD database, including 1,573 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.011 (93 hom., cov: 10)
  • Exomes 𝑓: 0.010 (1480 hom.)
• Consequence: FCGR3B NM_001244753.2 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.273

Genes affected

FCGR3B (HGNC:3620): (Fc gamma receptor IIIb) The protein encoded by this gene is a low affinity receptor for the Fc region of gamma immunoglobulins (IgG). The encoded protein acts as a monomer and can bind either monomeric or aggregated IgG. This gene may function to capture immune complexes in the peripheral circulation. Several transcript variants encoding different isoforms have been found for this gene. A highly-similar gene encoding a related protein is also found on chromosome 1. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 1-161629785-G-T is Benign according to our data. Variant chr1-161629785-G-T is described in ClinVar as [Benign]. Clinvar id is 2639515.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-161629785-G-T is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=0.273 with no splicing effect.
• BS2: High Homozygotes in GnomAd at 93 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR3B	NM_001244753.2	c.312C>A	p.Val104=	synonymous_variant	3/5	ENST00000650385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCGR3B	ENST00000650385.1	c.312C>A	p.Val104=	synonymous_variant	3/5		NM_001244753.2	P2

Frequencies

GnomAD3 genomes AF: 0.0108 AC: 834 AN: 76938 Hom.: 93 Cov.: 10

Gnomad AFR AF: 0.00291

Gnomad AMI AF: 0.0372

Gnomad AMR AF: 0.00859

Gnomad ASJ AF: 0.00207

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00363

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.00450

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.0102

GnomAD3 exomes AF: 0.00920 AC: 2108 AN: 229208 Hom.: 195 AF XY: 0.00922 AC XY: 1152 AN XY: 124954

Gnomad AFR exome AF: 0.00177

Gnomad AMR exome AF: 0.00357

Gnomad ASJ exome AF: 0.00102

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00339

Gnomad FIN exome AF: 0.0325

Gnomad NFE exome AF: 0.0111

Gnomad OTH exome AF: 0.00739

GnomAD4 exome AF: 0.0103 AC: 13944 AN: 1354350 Hom.: 1480 Cov.: 30 AF XY: 0.0102 AC XY: 6825 AN XY: 672076

Gnomad4 AFR exome AF: 0.00150

Gnomad4 AMR exome AF: 0.00410

Gnomad4 ASJ exome AF: 0.00128

Gnomad4 EAS exome AF: 0.0000347

Gnomad4 SAS exome AF: 0.00440

Gnomad4 FIN exome AF: 0.0320

Gnomad4 NFE exome AF: 0.0109

Gnomad4 OTH exome AF: 0.00785

GnomAD4 genome AF: 0.0108 AC: 832 AN: 76988 Hom.: 93 Cov.: 10 AF XY: 0.0112 AC XY: 404 AN XY: 36116

Gnomad4 AFR AF: 0.00290

Gnomad4 AMR AF: 0.00842

Gnomad4 ASJ AF: 0.00207

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00302

Gnomad4 FIN AF: 0.0379

Gnomad4 NFE AF: 0.0124

Gnomad4 OTH AF: 0.0101

Alfa AF: 0.00611 Hom.: 14

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2022

FCGR3B: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	6.9
Dann	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs200303549; hg19: chr1-161599575;