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:

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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 = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
FCER1A	NM_001387280.1 link	c.589+118C>T	intron_variant	Intron 4 of 4	ENST00000693622.1	NP_001374209.1
FCER1A	NM_002001.4 link	c.589+118C>T	intron_variant	Intron 6 of 6		NP_001992.1	P12319
FCER1A	NM_001387282.1 link	c.490+118C>T	intron_variant	Intron 4 of 4		NP_001374211.1
FCER1A	NM_001387281.1 link	c.334+118C>T	intron_variant	Intron 3 of 3		NP_001374210.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FCER1A	ENST00000693622.1 link	c.589+118C>T	intron_variant	Intron 4 of 4		NM_001387280.1	ENSP00000509626.1	P12319
FCER1A	ENST00000368115.5 link	c.589+118C>T	intron_variant	Intron 5 of 5	1		ENSP00000357097.1	P12319
FCER1A	ENST00000368114.1 link	c.490+118C>T	intron_variant	Intron 4 of 4	3		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 v4.3

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

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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