Genetic Variant NM_001220500.2:c.470-128C>T (chr19-7690685-G-A) – 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.470-128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 871,008 control chromosomes in the GnomAD database, including 38,400 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 ( 10423 hom., cov: 32)

Exomes 𝑓: 0.27 ( 27977 hom. )

Consequence

FCER2
NM_001220500.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.281

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
FCER2	NM_001220500.2 link	c.470-128C>T	intron_variant	Intron 8 of 10	ENST00000597921.6	NP_001207429.1	P06734
FCER2	NM_002002.5 link	c.470-128C>T	intron_variant	Intron 8 of 10		NP_001993.2	P06734
FCER2	NM_001207019.3 link	c.467-128C>T	intron_variant	Intron 7 of 9		NP_001193948.2	P06734K3W4U1
FCER2	XM_005272462.5 link	c.470-128C>T	intron_variant	Intron 8 of 10		XP_005272519.1	P06734

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER2	ENST00000597921.6 link	c.470-128C>T		intron_variant	Intron 8 of 10	1	NM_001220500.2	ENSP00000471974.1		P06734

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53061

AN:

151740

Hom.:

10402

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:

0.386

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.349

GnomAD4 exome

AF:

0.270

AC:

194033

AN:

719150

Hom.:

27977

AF XY:

0.275

AC XY:

101130

AN XY:

367470

show subpopulations

African (AFR)

AF:

0.522

AC:

9036

AN:

17314

American (AMR)

AF:

0.193

AC:

4761

AN:

24606

Ashkenazi Jewish (ASJ)

AF:

0.319

AC:

5181

AN:

16220

East Asian (EAS)

AF:

0.282

AC:

9120

AN:

32374

South Asian (SAS)

AF:

0.357

AC:

19743

AN:

55262

European-Finnish (FIN)

AF:

0.236

AC:

7500

AN:

31788

Middle Eastern (MID)

AF:

0.349

AC:

912

AN:

2612

European-Non Finnish (NFE)

AF:

0.253

AC:

127321

AN:

504034

Other (OTH)

AF:

0.299

AC:

10459

AN:

34940

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

6896

13792

20688

27584

34480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2798

5596

8394

11192

13990

<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:

53112

AN:

151858

Hom.:

10423

Cov.:

AF XY:

0.346

AC XY:

25698

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.528

AC:

21853

AN:

41376

American (AMR)

AF:

0.254

AC:

3879

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1103

AN:

3470

East Asian (EAS)

AF:

0.344

AC:

1770

AN:

5142

South Asian (SAS)

AF:

0.377

AC:

1814

AN:

4814

European-Finnish (FIN)

AF:

0.234

AC:

2480

AN:

10582

Middle Eastern (MID)

AF:

0.378

AC:

111

AN:

294

European-Non Finnish (NFE)

AF:

0.281

AC:

19060

AN:

67908

Other (OTH)

AF:

0.344

AC:

724

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1624

3248

4871

6495

8119

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:

0.183

Hom.:

406

Bravo

AF:

0.356

Asia WGS

AF:

0.346

AC:

1200

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.4

(source)

DANN

Benign

0.57

PhyloP100

-0.28

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over