Variant chr1-159304153-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001387280.1(FCER1A):c.302G>A(p.Ser101Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00341 in 1,613,892 control chromosomes in the GnomAD database, including 189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0036 ( 19 hom., cov: 32)

Exomes 𝑓: 0.0034 ( 170 hom. )

Consequence

FCER1A
NM_001387280.1 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.58

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 made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0032084882).

BP6

Variant 1-159304153-G-A is Benign according to our data. Variant chr1-159304153-G-A is described in ClinVar as [Benign]. Clinvar id is 787858.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
FCER1A	NM_001387280.1 linkuse as main transcript	c.302G>A	p.Ser101Asn	missense_variant	3/5	ENST00000693622.1	NP_001374209.1
FCER1A	NM_002001.4 linkuse as main transcript	c.302G>A	p.Ser101Asn	missense_variant	5/7		NP_001992.1
FCER1A	NM_001387282.1 linkuse as main transcript	c.203G>A	p.Ser68Asn	missense_variant	3/5		NP_001374211.1
FCER1A	NM_001387281.1 linkuse as main transcript	c.76+1279G>A		intron_variant			NP_001374210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
FCER1A	ENST00000693622.1 linkuse as main transcript	c.302G>A	p.Ser101Asn	missense_variant	3/5		NM_001387280.1	ENSP00000509626	P1
FCER1A	ENST00000368115.5 linkuse as main transcript	c.302G>A	p.Ser101Asn	missense_variant	4/6	1		ENSP00000357097	P1
FCER1A	ENST00000368114.1 linkuse as main transcript	c.203G>A	p.Ser68Asn	missense_variant	3/5	3		ENSP00000357096

Frequencies

GnomAD3 genomes

AF:

0.00365

AC:

555

AN:

152200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000169

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000589

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.0775

Gnomad SAS

AF:

0.00641

Gnomad FIN

AF:

0.00216

Gnomad MID

AF:

0.00955

Gnomad NFE

AF:

0.000779

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.00637

AC:

1597

AN:

250848

Hom.:

AF XY:

0.00620

AC XY:

840

AN XY:

135524

show subpopulations

Gnomad AFR exome

AF:

0.0000615

Gnomad AMR exome

AF:

0.000463

Gnomad ASJ exome

AF:

0.00239

Gnomad EAS exome

AF:

0.0693

Gnomad SAS exome

AF:

0.00412

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.000918

Gnomad OTH exome

AF:

0.00458

GnomAD4 exome

AF:

0.00338

AC:

4944

AN:

1461574

Hom.:

170

Cov.:

AF XY:

0.00341

AC XY:

2480

AN XY:

727104

show subpopulations

Gnomad4 AFR exome

AF:

0.000149

Gnomad4 AMR exome

AF:

0.000604

Gnomad4 ASJ exome

AF:

0.00237

Gnomad4 EAS exome

AF:

0.0850

Gnomad4 SAS exome

AF:

0.00459

Gnomad4 FIN exome

AF:

0.00135

Gnomad4 NFE exome

AF:

0.000592

Gnomad4 OTH exome

AF:

0.00543

GnomAD4 genome

AF:

0.00362

AC:

552

AN:

152318

Hom.:

Cov.:

AF XY:

0.00405

AC XY:

302

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.000168

Gnomad4 AMR

AF:

0.000589

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.0773

Gnomad4 SAS

AF:

0.00642

Gnomad4 FIN

AF:

0.00216

Gnomad4 NFE

AF:

0.000779

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00355

Hom.:

Bravo

AF:

0.00387

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.000778

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00116

AC:

ExAC

AF:

0.00628

AC:

762

Asia WGS

AF:

0.0260

AC:

AN:

3478

EpiCase

AF:

0.00131

EpiControl

AF:

0.00190

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 04, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.69

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Uncertain

0.74

D;.

Eigen

Uncertain

0.44

Eigen_PC

Benign

0.20

FATHMM_MKL

Uncertain

0.85

LIST_S2

Benign

0.45

T;T

MetaRNN

Benign

0.0032

T;T

MetaSVM

Benign

-0.55

MutationAssessor

Pathogenic

4.0

H;.

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.44

PROVEAN

Uncertain

-2.8

D;D

REVEL

Benign

0.16

Sift

Pathogenic

0.0

D;D

Sift4G

Pathogenic

0.0

D;D

Polyphen

1.0

D;.

Vest4

0.48

MVP

0.56

MPC

0.20

ClinPred

0.15

GERP RS

3.8

Varity_R

0.58

gMVP

0.61

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over