Variant chr1-161506414-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001136219.3(FCGR2A):c.187C>T(p.Gln63*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,614,092 control chromosomes in the GnomAD database, including 11,453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.090 ( 849 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10604 hom. )

Consequence

FCGR2A
NM_001136219.3 stop_gained

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.500

Variant links:

Genes affected

FCGR2A (HGNC:3616): (Fc gamma receptor IIa) This gene encodes one member of a family of immunoglobulin Fc receptor genes found on the surface of many immune response cells. The protein encoded by this gene is a cell surface receptor found on phagocytic cells such as macrophages and neutrophils, and is involved in the process of phagocytosis and clearing of immune complexes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2008]

FCGR2A links:

FCGR2A (HGNC:):

FCGR2A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 1-161506414-C-T is Benign according to our data. Variant chr1-161506414-C-T is described in ClinVar as [Benign]. Clinvar id is 402852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-161506414-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCGR2A	NM_001136219.3 linkuse as main transcript	c.187C>T	p.Gln63*	stop_gained	3/7	ENST00000271450.12	NP_001129691.1	P12318-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCGR2A	ENST00000271450.12 linkuse as main transcript	c.187C>T	p.Gln63*	stop_gained	3/7	1	NM_001136219.3	ENSP00000271450.6		P12318-1

Frequencies

GnomAD3 genomes

AF:

0.0897

AC:

13645

AN:

152118

Hom.:

847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0263

Gnomad AMI

AF:

0.0779

Gnomad AMR

AF:

0.0979

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0847

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.104

AC:

26117

AN:

251418

Hom.:

1800

AF XY:

0.109

AC XY:

14744

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.0250

Gnomad AMR exome

AF:

0.0637

Gnomad ASJ exome

AF:

0.256

Gnomad EAS exome

AF:

0.000490

Gnomad SAS exome

AF:

0.0890

Gnomad FIN exome

AF:

0.120

Gnomad NFE exome

AF:

0.130

Gnomad OTH exome

AF:

0.132

GnomAD4 exome

AF:

0.114

AC:

166943

AN:

1461856

Hom.:

10604

Cov.:

AF XY:

0.115

AC XY:

83596

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.0250

Gnomad4 AMR exome

AF:

0.0668

Gnomad4 ASJ exome

AF:

0.259

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.0918

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.121

Gnomad4 OTH exome

AF:

0.113

GnomAD4 genome

AF:

0.0896

AC:

13647

AN:

152236

Hom.:

849

Cov.:

AF XY:

0.0902

AC XY:

6714

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0263

Gnomad4 AMR

AF:

0.0977

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0848

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.0994

Alfa

AF:

0.120

Hom.:

571

Bravo

AF:

0.0888

TwinsUK

AF:

0.124

AC:

459

ALSPAC

AF:

0.122

AC:

471

ESP6500AA

AF:

0.0291

AC:

128

ESP6500EA

AF:

0.132

AC:

1131

ExAC

AF:

0.103

AC:

12529

Asia WGS

AF:

0.0330

AC:

117

AN:

3478

EpiCase

AF:

0.142

EpiControl

AF:

0.146

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

FCGR2A-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 10, 2020

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.62

CADD

Pathogenic

DANN

Benign

0.81

Eigen

Benign

-0.63

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.022

Vest4

0.62

GERP RS

-2.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over