dbSNP rs2277992: 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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
FCER2	NM_001220500.2 link	c.470-139T>C	intron_variant	Intron 8 of 10	ENST00000597921.6	NP_001207429.1
FCER2	NM_002002.5 link	c.470-139T>C	intron_variant	Intron 8 of 10		NP_001993.2
FCER2	NM_001207019.3 link	c.467-139T>C	intron_variant	Intron 7 of 9		NP_001193948.2
FCER2	XM_005272462.5 link	c.470-139T>C	intron_variant	Intron 8 of 10		XP_005272519.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER2	ENST00000597921.6 link	c.470-139T>C		intron_variant	Intron 8 of 10	1	NM_001220500.2	ENSP00000471974.1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over