Variant 1-161510859-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001136219.3(FCGR2A):c.645A>G(p.Pro215Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,614,006 control chromosomes in the GnomAD database, including 11,351 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.088 ( 869 hom., cov: 33)

Exomes 𝑓: 0.11 ( 10482 hom. )

Consequence

FCGR2A
NM_001136219.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.233

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 1-161510859-A-G is Benign according to our data. Variant chr1-161510859-A-G is described in ClinVar as [Benign]. Clinvar id is 402854.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.233 with no splicing effect.

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.645A>G	p.Pro215Pro	synonymous_variant	5/7	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.645A>G	p.Pro215Pro	synonymous_variant	5/7	1	NM_001136219.3	ENSP00000271450.6		P12318-1

Frequencies

GnomAD3 genomes

AF:

0.0883

AC:

13434

AN:

152092

Hom.:

869

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0213

Gnomad AMI

AF:

0.0779

Gnomad AMR

AF:

0.0988

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0853

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.103

AC:

25952

AN:

251426

Hom.:

1790

AF XY:

0.108

AC XY:

14680

AN XY:

135882

show subpopulations

Gnomad AFR exome

AF:

0.0191

Gnomad AMR exome

AF:

0.0643

Gnomad ASJ exome

AF:

0.248

Gnomad EAS exome

AF:

0.000381

Gnomad SAS exome

AF:

0.0892

Gnomad FIN exome

AF:

0.119

Gnomad NFE exome

AF:

0.130

Gnomad OTH exome

AF:

0.131

GnomAD4 exome

AF:

0.114

AC:

166188

AN:

1461796

Hom.:

10482

Cov.:

AF XY:

0.114

AC XY:

83244

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.0183

Gnomad4 AMR exome

AF:

0.0672

Gnomad4 ASJ exome

AF:

0.251

Gnomad4 EAS exome

AF:

0.000176

Gnomad4 SAS exome

AF:

0.0920

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.121

Gnomad4 OTH exome

AF:

0.111

GnomAD4 genome

AF:

0.0882

AC:

13428

AN:

152210

Hom.:

869

Cov.:

AF XY:

0.0890

AC XY:

6621

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0212

Gnomad4 AMR

AF:

0.0986

Gnomad4 ASJ

AF:

0.244

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0854

Gnomad4 FIN

AF:

0.109

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.0999

Alfa

AF:

0.129

Hom.:

592

Bravo

AF:

0.0867

Asia WGS

AF:

0.0290

AC:

105

AN:

3478

EpiCase

AF:

0.142

EpiControl

AF:

0.147

ClinVar

Significance: Benign

Submissions summary: Benign:2

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.2

DANN

Benign

0.39

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