Variant rs7529425 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000271450.12(FCGR2A):c.365-11G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,613,708 control chromosomes in the GnomAD database, including 11,631 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.098 ( 915 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10716 hom. )

Consequence

FCGR2A
ENST00000271450.12 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00001120

Clinical Significance

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

Conservation

PhyloP100: -0.353

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 made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 1-161509809-G-A is Benign according to our data. Variant chr1-161509809-G-A is described in ClinVar as [Benign]. Clinvar id is 402853.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 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.365-11G>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000271450.12	NP_001129691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCGR2A	ENST00000271450.12 linkuse as main transcript	c.365-11G>A		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001136219.3	ENSP00000271450	A2	P12318-1

Frequencies

GnomAD3 genomes

AF:

0.0981

AC:

14913

AN:

152032

Hom.:

913

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0525

Gnomad AMI

AF:

0.0779

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0852

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.110

GnomAD3 exomes

AF:

0.106

AC:

26746

AN:

251380

Hom.:

1853

AF XY:

0.111

AC XY:

15036

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.0522

Gnomad AMR exome

AF:

0.0668

Gnomad ASJ exome

AF:

0.256

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0888

Gnomad FIN exome

AF:

0.120

Gnomad NFE exome

AF:

0.131

Gnomad OTH exome

AF:

0.132

GnomAD4 exome

AF:

0.115

AC:

168579

AN:

1461558

Hom.:

10716

Cov.:

AF XY:

0.116

AC XY:

84306

AN XY:

727094

show subpopulations

Gnomad4 AFR exome

AF:

0.0501

Gnomad4 AMR exome

AF:

0.0700

Gnomad4 ASJ exome

AF:

0.259

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0918

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.121

Gnomad4 OTH exome

AF:

0.116

GnomAD4 genome

AF:

0.0980

AC:

14914

AN:

152150

Hom.:

915

Cov.:

AF XY:

0.0986

AC XY:

7332

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.0525

Gnomad4 AMR

AF:

0.104

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0851

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.123

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.135

Hom.:

1569

Bravo

AF:

0.0984

Asia WGS

AF:

0.0350

AC:

123

AN:

3478

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

-0.71

CADD

Benign

2.4

DANN

Benign

0.47

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000011

dbscSNV1_RF

Benign

0.0040

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