Genetic Variant FCER2:c.22+79dupG (chr19-7699659-G-GC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001220500.2(FCER2):c.22+79dupG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.63 ( 30553 hom., cov: 0)

Exomes 𝑓: 0.65 ( 262362 hom. )

Consequence

FCER2
NM_001220500.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.94

Publications

4 publications found

Variant links:

Genes affected

FCER2 (HGNC:3612): (Fc epsilon receptor II) The protein encoded by this gene is a B-cell specific antigen, and a low-affinity receptor for IgE. It has essential roles in B cell growth and differentiation, and the regulation of IgE production. This protein also exists as a soluble secreted form, then functioning as a potent mitogenic growth factor. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Jul 2011]

FCER2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001220500.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FCER2	NM_001220500.2	MANE Select	c.22+79dupG	intron	N/A	NP_001207429.1
FCER2	NM_002002.5		c.22+79dupG	intron	N/A	NP_001993.2
FCER2	NM_001207019.3		c.-265dupG	upstream_gene	N/A	NP_001193948.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FCER2	ENST00000597921.6	TSL:1 MANE Select	c.22+79_22+80insG	intron	N/A	ENSP00000471974.1
FCER2	ENST00000346664.9	TSL:1	c.22+79_22+80insG	intron	N/A	ENSP00000264072.6
FCER2	ENST00000593418.1	TSL:3	c.22+79_22+80insG	intron	N/A	ENSP00000472067.1

Frequencies

GnomAD3 genomes

AF:

0.632

AC:

95496

AN:

151156

Hom.:

30518

Cov.:

show subpopulations

Gnomad AFR

AF:

0.562

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.660

Gnomad ASJ

AF:

0.686

Gnomad EAS

AF:

0.835

Gnomad SAS

AF:

0.737

Gnomad FIN

AF:

0.671

Gnomad MID

AF:

0.674

Gnomad NFE

AF:

0.638

Gnomad OTH

AF:

0.646

GnomAD4 exome

AF:

0.645

AC:

801699

AN:

1242430

Hom.:

262362

Cov.:

AF XY:

0.649

AC XY:

408387

AN XY:

629282

show subpopulations

African (AFR)

AF:

0.554

AC:

16085

AN:

29050

American (AMR)

AF:

0.641

AC:

28425

AN:

44346

Ashkenazi Jewish (ASJ)

AF:

0.695

AC:

17165

AN:

24688

East Asian (EAS)

AF:

0.842

AC:

32634

AN:

38738

South Asian (SAS)

AF:

0.736

AC:

60165

AN:

81724

European-Finnish (FIN)

AF:

0.675

AC:

35962

AN:

53248

Middle Eastern (MID)

AF:

0.668

AC:

3440

AN:

5150

European-Non Finnish (NFE)

AF:

0.628

AC:

573065

AN:

912264

Other (OTH)

AF:

0.653

AC:

34758

AN:

53222

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

13945

27891

41836

55782

69727

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14032

28064

42096

56128

70160

<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:

0.632

AC:

95592

AN:

151274

Hom.:

30553

Cov.:

AF XY:

0.636

AC XY:

46960

AN XY:

73876

show subpopulations

African (AFR)

AF:

0.562

AC:

23119

AN:

41120

American (AMR)

AF:

0.661

AC:

10031

AN:

15186

Ashkenazi Jewish (ASJ)

AF:

0.686

AC:

2381

AN:

3470

East Asian (EAS)

AF:

0.835

AC:

4246

AN:

5082

South Asian (SAS)

AF:

0.738

AC:

3545

AN:

4804

European-Finnish (FIN)

AF:

0.671

AC:

6998

AN:

10424

Middle Eastern (MID)

AF:

0.677

AC:

199

AN:

294

European-Non Finnish (NFE)

AF:

0.638

AC:

43329

AN:

67878

Other (OTH)

AF:

0.648

AC:

1364

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

1718

3436

5155

6873

8591

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<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:

0.637

Hom.:

3816

Bravo

AF:

0.623

Asia WGS

AF:

0.790

AC:

2745

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-2.9

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