Variant 1-161589676-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The ENST00000466542.6(FCGR2C):c.248C>A(p.Pro83Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 8/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0041 ( 21 hom., cov: 29)

Exomes 𝑓: 0.0026 ( 872 hom. )

Failed GnomAD Quality Control

Consequence

FCGR2C
ENST00000466542.6 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.608

Variant links:

Genes affected

FCGR2C (HGNC:15626): (Fc gamma receptor IIc (gene/pseudogene)) This gene encodes one of three members of a family of low-affinity immunoglobulin gamma Fc receptors found on the surface of many immune response cells. The encoded protein is a transmembrane glycoprotein and may be involved in phagocytosis and clearing of immune complexes. An allelic polymorphism in this gene results in both coding and non-coding variants. [provided by RefSeq, Apr 2012]

FCGR2C links:

ENSG00000289768 (HGNC:):

ENSG00000289768 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.018492132).

BP6

Variant 1-161589676-C-A is Benign according to our data. Variant chr1-161589676-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2397613.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCGR2C	NR_047648.1 linkuse as main transcript	n.347C>A		non_coding_transcript_exon_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCGR2C	ENST00000466542.6 linkuse as main transcript	c.248C>A	p.Pro83Gln	missense_variant	3/7	1		ENSP00000426627.1
ENSG00000289768	ENST00000699402.1 linkuse as main transcript	c.41-40645G>T		intron_variant				ENSP00000514363.1		A0A8V8TN80

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

595

AN:

143550

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00151

Gnomad AMI

AF:

0.00111

Gnomad AMR

AF:

0.00500

Gnomad ASJ

AF:

0.0109

Gnomad EAS

AF:

0.00117

Gnomad SAS

AF:

0.00729

Gnomad FIN

AF:

0.000203

Gnomad MID

AF:

0.0167

Gnomad NFE

AF:

0.00570

Gnomad OTH

AF:

0.00830

GnomAD3 exomes

AF:

0.00162

AC:

392

AN:

242532

Hom.:

125

AF XY:

0.00154

AC XY:

202

AN XY:

130912

show subpopulations

Gnomad AFR exome

AF:

0.00114

Gnomad AMR exome

AF:

0.00103

Gnomad ASJ exome

AF:

0.00327

Gnomad EAS exome

AF:

0.000819

Gnomad SAS exome

AF:

0.00181

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00198

Gnomad OTH exome

AF:

0.00410

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00260

AC:

3650

AN:

1404860

Hom.:

872

Cov.:

AF XY:

0.00266

AC XY:

1856

AN XY:

698456

show subpopulations

Gnomad4 AFR exome

AF:

0.00151

Gnomad4 AMR exome

AF:

0.00162

Gnomad4 ASJ exome

AF:

0.00701

Gnomad4 EAS exome

AF:

0.000834

Gnomad4 SAS exome

AF:

0.00231

Gnomad4 FIN exome

AF:

0.000448

Gnomad4 NFE exome

AF:

0.00268

Gnomad4 OTH exome

AF:

0.00381

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00411

AC:

591

AN:

143664

Hom.:

Cov.:

AF XY:

0.00385

AC XY:

269

AN XY:

69926

show subpopulations

Gnomad4 AFR

AF:

0.00150

Gnomad4 AMR

AF:

0.00499

Gnomad4 ASJ

AF:

0.0109

Gnomad4 EAS

AF:

0.00117

Gnomad4 SAS

AF:

0.00686

Gnomad4 FIN

AF:

0.000203

Gnomad4 NFE

AF:

0.00571

Gnomad4 OTH

AF:

0.00719

Alfa

AF:

0.00461

Hom.:

TwinsUK

AF:

0.0108

AC:

ALSPAC

AF:

0.00960

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000599

AC:

ExAC

AF:

0.00163

AC:

194

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 15, 2021

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

FCGR2C: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.36

CADD

Benign

0.0020

DANN

Benign

0.78

FATHMM_MKL

Benign

0.0050

LIST_S2

Benign

0.045

T;T

MetaRNN

Benign

0.018

T;T

Vest4

0.15

MVP

0.030

GERP RS

-2.3

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