Genetic Variant FCER2:c.470-75T>C (chr19-7690632-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.470-75T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 1,486,002 control chromosomes in the GnomAD database, including 65,361 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 ( 10421 hom., cov: 32)

Exomes 𝑓: 0.28 ( 54940 hom. )

Consequence

FCER2
NM_001220500.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.25

Publications

3 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 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.470-75T>C	intron	N/A	NP_001207429.1	P06734
FCER2	NM_002002.5		c.470-75T>C	intron	N/A	NP_001993.2
FCER2	NM_001207019.3		c.467-75T>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.470-75T>C	intron	N/A	ENSP00000471974.1	P06734
FCER2	ENST00000346664.9	TSL:1	c.470-75T>C	intron	N/A	ENSP00000264072.6	P06734
FCER2	ENST00000360067.8	TSL:5	c.467-75T>C	intron	N/A	ENSP00000353178.4	K3W4U1

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53075

AN:

151716

Hom.:

10400

Cov.:

show subpopulations

Gnomad AFR

AF:

0.528

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.344

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.385

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.349

GnomAD4 exome

AF:

0.282

AC:

376255

AN:

1334168

Hom.:

54940

AF XY:

0.285

AC XY:

187942

AN XY:

660150

show subpopulations

African (AFR)

AF:

0.536

AC:

16470

AN:

30716

American (AMR)

AF:

0.170

AC:

6445

AN:

37914

Ashkenazi Jewish (ASJ)

AF:

0.320

AC:

7201

AN:

22520

East Asian (EAS)

AF:

0.288

AC:

10817

AN:

37540

South Asian (SAS)

AF:

0.358

AC:

26940

AN:

75240

European-Finnish (FIN)

AF:

0.232

AC:

9319

AN:

40190

Middle Eastern (MID)

AF:

0.375

AC:

1754

AN:

4672

European-Non Finnish (NFE)

AF:

0.272

AC:

280243

AN:

1029588

Other (OTH)

AF:

0.306

AC:

17066

AN:

55788

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

11391

22781

34172

45562

56953

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9522

19044

28566

38088

47610

<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:

0.350

AC:

53126

AN:

151834

Hom.:

10421

Cov.:

AF XY:

0.347

AC XY:

25704

AN XY:

74172

show subpopulations

African (AFR)

AF:

0.528

AC:

21856

AN:

41386

American (AMR)

AF:

0.255

AC:

3883

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1103

AN:

3468

East Asian (EAS)

AF:

0.345

AC:

1780

AN:

5162

South Asian (SAS)

AF:

0.377

AC:

1816

AN:

4822

European-Finnish (FIN)

AF:

0.234

AC:

2473

AN:

10550

Middle Eastern (MID)

AF:

0.377

AC:

110

AN:

292

European-Non Finnish (NFE)

AF:

0.281

AC:

19062

AN:

67882

Other (OTH)

AF:

0.344

AC:

726

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1642

3284

4927

6569

8211

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.317

Hom.:

1068

Bravo

AF:

0.356

Asia WGS

AF:

0.346

AC:

1200

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.0090

(source)

DANN

Benign

0.34

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