Genetic Variant FCER1A:c.589+118C>T (chr1-159306363-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001387280.1(FCER1A):c.589+118C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 907,100 control chromosomes in the GnomAD database, including 156,426 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 0.65 ( 33892 hom., cov: 31)

Exomes 𝑓: 0.56 ( 122534 hom. )

Consequence

FCER1A
NM_001387280.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.514

Publications

17 publications found

Variant links:

Genes affected

FCER1A (HGNC:3609): (Fc epsilon receptor Ia) The immunoglobulin epsilon receptor (IgE receptor) is the initiator of the allergic response. When two or more high-affinity IgE receptors are brought together by allergen-bound IgE molecules, mediators such as histamine that are responsible for allergy symptoms are released. This receptor is comprised of an alpha subunit, a beta subunit, and two gamma subunits. The protein encoded by this gene represents the alpha subunit. [provided by RefSeq, Aug 2011]

FCER1A 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387280.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FCER1A	NM_001387280.1	MANE Select	c.589+118C>T	intron	N/A	NP_001374209.1	P12319
FCER1A	NM_002001.4		c.589+118C>T	intron	N/A	NP_001992.1	P12319
FCER1A	NM_001387282.1		c.490+118C>T	intron	N/A	NP_001374211.1	E9PRN1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FCER1A	ENST00000693622.1	MANE Select	c.589+118C>T	intron	N/A	ENSP00000509626.1	P12319
FCER1A	ENST00000368115.5	TSL:1	c.589+118C>T	intron	N/A	ENSP00000357097.1	P12319
FCER1A	ENST00000368114.1	TSL:3	c.490+118C>T	intron	N/A	ENSP00000357096.1	E9PRN1

Frequencies

GnomAD3 genomes

AF:

0.648

AC:

98421

AN:

151928

Hom.:

33851

Cov.:

show subpopulations

Gnomad AFR

AF:

0.891

Gnomad AMI

AF:

0.495

Gnomad AMR

AF:

0.528

Gnomad ASJ

AF:

0.503

Gnomad EAS

AF:

0.742

Gnomad SAS

AF:

0.476

Gnomad FIN

AF:

0.536

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.559

Gnomad OTH

AF:

0.626

GnomAD4 exome

AF:

0.561

AC:

423850

AN:

755054

Hom.:

122534

AF XY:

0.558

AC XY:

215735

AN XY:

386932

show subpopulations

African (AFR)

AF:

0.904

AC:

16182

AN:

17898

American (AMR)

AF:

0.495

AC:

10892

AN:

21990

Ashkenazi Jewish (ASJ)

AF:

0.509

AC:

8173

AN:

16060

East Asian (EAS)

AF:

0.782

AC:

25853

AN:

33048

South Asian (SAS)

AF:

0.467

AC:

24893

AN:

53360

European-Finnish (FIN)

AF:

0.559

AC:

21326

AN:

38164

Middle Eastern (MID)

AF:

0.571

AC:

1484

AN:

2598

European-Non Finnish (NFE)

AF:

0.549

AC:

294165

AN:

535582

Other (OTH)

AF:

0.574

AC:

20882

AN:

36354

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

9097

18194

27290

36387

45484

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5964

11928

17892

23856

29820

<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:

0.648

AC:

98514

AN:

152046

Hom.:

33892

Cov.:

AF XY:

0.640

AC XY:

47526

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.891

AC:

36987

AN:

41512

American (AMR)

AF:

0.528

AC:

8057

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.503

AC:

1746

AN:

3468

East Asian (EAS)

AF:

0.742

AC:

3831

AN:

5162

South Asian (SAS)

AF:

0.476

AC:

2293

AN:

4820

European-Finnish (FIN)

AF:

0.536

AC:

5660

AN:

10556

Middle Eastern (MID)

AF:

0.562

AC:

164

AN:

292

European-Non Finnish (NFE)

AF:

0.559

AC:

38012

AN:

67954

Other (OTH)

AF:

0.623

AC:

1313

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1607

3214

4821

6428

8035

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

766

1532

2298

3064

3830

<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:

0.584

Hom.:

110894

Bravo

AF:

0.660

Asia WGS

AF:

0.546

AC:

1900

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.83

(source)

DANN

Benign

0.62

PhyloP100

-0.51

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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