Variant chr1-161518073-C-T 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.879C>T(p.Pro293Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,609,480 control chromosomes in the GnomAD database, including 6,199 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.089 ( 416 hom., cov: 32)

Exomes 𝑓: 0.11 ( 5783 hom. )

Consequence

FCGR2A
NM_001136219.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.389

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:

ENSG00000273112 (HGNC:):

ENSG00000273112 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 1-161518073-C-T is Benign according to our data. Variant chr1-161518073-C-T is described in ClinVar as [Benign]. Clinvar id is 402855.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.389 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCGR2A	NM_001136219.3 link	c.879C>T	p.Pro293Pro	synonymous_variant	Exon 7 of 7	ENST00000271450.12	NP_001129691.1	P12318-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCGR2A	ENST00000271450.12 link	c.879C>T	p.Pro293Pro	synonymous_variant	Exon 7 of 7	1	NM_001136219.3	ENSP00000271450.6		P12318-1

Frequencies

GnomAD3 genomes

AF:

0.0892

AC:

13515

AN:

151482

Hom.:

417

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0326

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.0993

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.234

Gnomad SAS

AF:

0.0947

Gnomad FIN

AF:

0.0637

Gnomad MID

AF:

0.103

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.115

AC:

28660

AN:

250282

Hom.:

1536

AF XY:

0.114

AC XY:

15477

AN XY:

135280

show subpopulations

Gnomad AFR exome

AF:

0.0319

Gnomad AMR exome

AF:

0.117

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.251

Gnomad SAS exome

AF:

0.0938

Gnomad FIN exome

AF:

0.0675

Gnomad NFE exome

AF:

0.116

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.108

AC:

157658

AN:

1457880

Hom.:

5783

Cov.:

AF XY:

0.108

AC XY:

78506

AN XY:

725326

show subpopulations

Gnomad4 AFR exome

AF:

0.0330

Gnomad4 AMR exome

AF:

0.113

Gnomad4 ASJ exome

AF:

0.140

Gnomad4 EAS exome

AF:

0.227

Gnomad4 SAS exome

AF:

0.0899

Gnomad4 FIN exome

AF:

0.0666

Gnomad4 NFE exome

AF:

0.108

Gnomad4 OTH exome

AF:

0.113

GnomAD4 genome

AF:

0.0891

AC:

13508

AN:

151600

Hom.:

416

Cov.:

AF XY:

0.0886

AC XY:

6570

AN XY:

74136

show subpopulations

Gnomad4 AFR

AF:

0.0326

Gnomad4 AMR

AF:

0.0991

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.234

Gnomad4 SAS

AF:

0.0946

Gnomad4 FIN

AF:

0.0637

Gnomad4 NFE

AF:

0.110

Gnomad4 OTH

AF:

0.0994

Alfa

AF:

0.112

Hom.:

225

Asia WGS

AF:

0.158

AC:

548

AN:

3476

EpiCase

AF:

0.126

EpiControl

AF:

0.124

ClinVar

Significance: Benign

Submissions summary: Benign:2

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.8

DANN

Benign

0.42

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