1-161506414-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -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

Publications

39 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 402852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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 rank	MANE	Protein	UniProt
FCGR2A	NM_001136219.3 link	c.187C>T	p.Gln63*	stop_gained	Exon 3 of 7	ENST00000271450.12	NP_001129691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCGR2A	ENST00000271450.12 link	c.187C>T	p.Gln63*	stop_gained	Exon 3 of 7	1	NM_001136219.3	ENSP00000271450.6

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

GnomAD2 exomes

AF:

0.104

AC:

26117

AN:

251418

AF XY:

0.109

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 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

African (AFR)

AF:

0.0250

AC:

837

AN:

33480

American (AMR)

AF:

0.0668

AC:

2986

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.259

AC:

6771

AN:

26136

East Asian (EAS)

AF:

0.000227

AC:

AN:

39672

South Asian (SAS)

AF:

0.0918

AC:

7921

AN:

86258

European-Finnish (FIN)

AF:

0.116

AC:

6194

AN:

53420

Middle Eastern (MID)

AF:

0.187

AC:

1077

AN:

5766

European-Non Finnish (NFE)

AF:

0.121

AC:

134333

AN:

1112006

Other (OTH)

AF:

0.113

AC:

6815

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

10645

21290

31935

42580

53225

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4684

9368

14052

18736

23420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0896

AC:

13647

AN:

152236

Hom.:

849

Cov.:

AF XY:

0.0902

AC XY:

6714

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.0263

AC:

1095

AN:

41562

American (AMR)

AF:

0.0977

AC:

1494

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.252

AC:

874

AN:

3472

East Asian (EAS)

AF:

0.000772

AC:

AN:

5184

South Asian (SAS)

AF:

0.0848

AC:

409

AN:

4822

European-Finnish (FIN)

AF:

0.110

AC:

1173

AN:

10616

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8275

AN:

67974

Other (OTH)

AF:

0.0994

AC:

210

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

633

1265

1898

2530

3163

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.101

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

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

FCGR2A-related disorder

Benign:1

Jan 10, 2020

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

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

(source)

DANN

Benign

0.81

Eigen

Benign

-0.63

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.022

PhyloP100

-0.50

Vest4

0.62

GERP RS

-2.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=185/15

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over