Genetic Variant FCER2:c.470-139T>C (chr19-7690696-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 NM_001220500.2(FCER2):c.470-139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 777,092 control chromosomes in the GnomAD database, including 34,473 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 0.35 ( 10191 hom., cov: 32)

Exomes 𝑓: 0.27 ( 24282 hom. )

Consequence

FCER2
NM_001220500.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420

Publications

2 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 -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 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	UniProt
FCER2	NM_001220500.2	MANE Select	c.470-139T>C	intron	N/A	NP_001207429.1	P06734
FCER2	NM_002002.5		c.470-139T>C	intron	N/A	NP_001993.2
FCER2	NM_001207019.3		c.467-139T>C	intron	N/A	NP_001193948.2	K3W4U1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FCER2	ENST00000597921.6	TSL:1 MANE Select	c.470-139T>C	intron	N/A	ENSP00000471974.1	P06734
FCER2	ENST00000346664.9	TSL:1	c.470-139T>C	intron	N/A	ENSP00000264072.6	P06734
FCER2	ENST00000360067.8	TSL:5	c.467-139T>C	intron	N/A	ENSP00000353178.4	K3W4U1

Frequencies

GnomAD3 genomes

AF:

0.346

AC:

52577

AN:

151754

Hom.:

10172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.517

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.344

Gnomad SAS

AF:

0.377

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.344

GnomAD4 exome

AF:

0.268

AC:

167550

AN:

625220

Hom.:

24282

AF XY:

0.273

AC XY:

87752

AN XY:

321816

show subpopulations

African (AFR)

AF:

0.506

AC:

7671

AN:

15152

American (AMR)

AF:

0.183

AC:

4080

AN:

22330

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

4739

AN:

15064

East Asian (EAS)

AF:

0.280

AC:

8911

AN:

31804

South Asian (SAS)

AF:

0.349

AC:

17881

AN:

51194

European-Finnish (FIN)

AF:

0.234

AC:

7285

AN:

31138

Middle Eastern (MID)

AF:

0.345

AC:

809

AN:

2346

European-Non Finnish (NFE)

AF:

0.252

AC:

106800

AN:

424490

Other (OTH)

AF:

0.296

AC:

9374

AN:

31702

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

5672

11344

17015

22687

28359

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1930

3860

5790

7720

9650

<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:

0.347

AC:

52627

AN:

151872

Hom.:

10191

Cov.:

AF XY:

0.343

AC XY:

25481

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.518

AC:

21420

AN:

41368

American (AMR)

AF:

0.252

AC:

3845

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1103

AN:

3470

East Asian (EAS)

AF:

0.344

AC:

1777

AN:

5166

South Asian (SAS)

AF:

0.376

AC:

1810

AN:

4820

European-Finnish (FIN)

AF:

0.233

AC:

2467

AN:

10570

Middle Eastern (MID)

AF:

0.378

AC:

111

AN:

294

European-Non Finnish (NFE)

AF:

0.281

AC:

19061

AN:

67918

Other (OTH)

AF:

0.339

AC:

716

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1624

3248

4872

6496

8120

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.327

Hom.:

1163

Bravo

AF:

0.352

Asia WGS

AF:

0.344

AC:

1196

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.4

(source)

DANN

Benign

0.39

PhyloP100

0.042

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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