Genetic Variant FCGR2C:c.134-25A>G (chr1-161589537-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000466542.6(FCGR2C):c.134-25A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,550,036 control chromosomes in the GnomAD database, including 458,326 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.70 ( 38077 hom., cov: 26)

Exomes 𝑓: 0.74 ( 420249 hom. )

Consequence

FCGR2C
ENST00000466542.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.21

Publications

17 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000466542.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCGR2C	NR_047648.1		n.233-25A>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FCGR2C	ENST00000466542.6	TSL:1	c.134-25A>G	intron	N/A	ENSP00000426627.1
ENSG00000289768	ENST00000699402.1		c.41-40506T>C	intron	N/A	ENSP00000514363.1	A0A8V8TN80
FCGR2C	ENST00000465075.6	TSL:1	n.226-25A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.702

AC:

98859

AN:

140840

Hom.:

38041

Cov.:

show subpopulations

Gnomad AFR

AF:

0.596

Gnomad AMI

AF:

0.618

Gnomad AMR

AF:

0.772

Gnomad ASJ

AF:

0.610

Gnomad EAS

AF:

0.763

Gnomad SAS

AF:

0.732

Gnomad FIN

AF:

0.806

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.733

Gnomad OTH

AF:

0.705

GnomAD2 exomes

AF:

0.741

AC:

177272

AN:

239272

AF XY:

0.738

show subpopulations

Gnomad AFR exome

AF:

0.596

Gnomad AMR exome

AF:

0.855

Gnomad ASJ exome

AF:

0.604

Gnomad EAS exome

AF:

0.752

Gnomad FIN exome

AF:

0.802

Gnomad NFE exome

AF:

0.729

Gnomad OTH exome

AF:

0.728

GnomAD4 exome

AF:

0.742

AC:

1046062

AN:

1409074

Hom.:

420249

Cov.:

AF XY:

0.740

AC XY:

518557

AN XY:

700402

show subpopulations

African (AFR)

AF:

0.602

AC:

19547

AN:

32484

American (AMR)

AF:

0.843

AC:

36913

AN:

43790

Ashkenazi Jewish (ASJ)

AF:

0.611

AC:

15021

AN:

24594

East Asian (EAS)

AF:

0.811

AC:

32094

AN:

39574

South Asian (SAS)

AF:

0.725

AC:

60908

AN:

84020

European-Finnish (FIN)

AF:

0.805

AC:

41296

AN:

51290

Middle Eastern (MID)

AF:

0.630

AC:

3378

AN:

5366

European-Non Finnish (NFE)

AF:

0.743

AC:

794995

AN:

1069740

Other (OTH)

AF:

0.720

AC:

41910

AN:

58216

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

10483

20967

31450

41934

52417

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18638

37276

55914

74552

93190

<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:

0.702

AC:

98945

AN:

140962

Hom.:

38077

Cov.:

AF XY:

0.705

AC XY:

48306

AN XY:

68494

show subpopulations

African (AFR)

AF:

0.596

AC:

22739

AN:

38140

American (AMR)

AF:

0.772

AC:

10804

AN:

13992

Ashkenazi Jewish (ASJ)

AF:

0.610

AC:

1948

AN:

3196

East Asian (EAS)

AF:

0.762

AC:

3854

AN:

5060

South Asian (SAS)

AF:

0.733

AC:

3256

AN:

4440

European-Finnish (FIN)

AF:

0.806

AC:

7626

AN:

9458

Middle Eastern (MID)

AF:

0.604

AC:

168

AN:

278

European-Non Finnish (NFE)

AF:

0.733

AC:

46651

AN:

63604

Other (OTH)

AF:

0.709

AC:

1345

AN:

1898

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

975

1950

2925

3900

4875

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<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:

0.709

Hom.:

8125

Asia WGS

AF:

0.755

AC:

2580

AN:

3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.57

(source)

DANN

Benign

0.36

PhyloP100

-2.2

Mutation Taster

=100/0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over