Genetic Variant FCER1G:c.50-111C>T (chr1-161217875-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_004106.2(FCER1G):c.50-111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 738,910 control chromosomes in the GnomAD database, including 33,241 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 0.31 ( 7602 hom., cov: 31)

Exomes 𝑓: 0.29 ( 25639 hom. )

Consequence

FCER1G
NM_004106.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05

Publications

40 publications found

Variant links:

Genes affected

FCER1G (HGNC:3611): (Fc epsilon receptor Ig) The high affinity IgE receptor is a key molecule involved in allergic reactions. It is a tetramer composed of 1 alpha, 1 beta, and 2 gamma chains. The gamma chains are also subunits of other Fc receptors. [provided by RefSeq, Jul 2008]

FCER1G 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004106.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCER1G	NM_004106.2	MANE Select	c.50-111C>T		intron	N/A	NP_004097.1	P30273

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FCER1G	ENST00000289902.2	TSL:1 MANE Select	c.50-111C>T	intron	N/A	ENSP00000289902.1	P30273
FCER1G	ENST00000882697.1		c.50-111C>T	intron	N/A	ENSP00000552756.1
FCER1G	ENST00000367992.7	TSL:3	c.50-111C>T	intron	N/A	ENSP00000356971.3	A6NCQ8

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

46777

AN:

151706

Hom.:

7585

Cov.:

show subpopulations

Gnomad AFR

AF:

0.381

Gnomad AMI

AF:

0.205

Gnomad AMR

AF:

0.331

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.429

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.323

GnomAD4 exome

AF:

0.287

AC:

168406

AN:

587086

Hom.:

25639

AF XY:

0.287

AC XY:

90206

AN XY:

314724

show subpopulations

African (AFR)

AF:

0.392

AC:

6332

AN:

16168

American (AMR)

AF:

0.373

AC:

12668

AN:

34004

Ashkenazi Jewish (ASJ)

AF:

0.279

AC:

4578

AN:

16410

East Asian (EAS)

AF:

0.450

AC:

16007

AN:

35574

South Asian (SAS)

AF:

0.357

AC:

21291

AN:

59642

European-Finnish (FIN)

AF:

0.286

AC:

13271

AN:

46380

Middle Eastern (MID)

AF:

0.309

AC:

1143

AN:

3694

European-Non Finnish (NFE)

AF:

0.244

AC:

84016

AN:

344310

Other (OTH)

AF:

0.294

AC:

9100

AN:

30904

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

6221

12441

18662

24882

31103

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1028

2056

3084

4112

5140

<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:

0.309

AC:

46840

AN:

151824

Hom.:

7602

Cov.:

AF XY:

0.312

AC XY:

23155

AN XY:

74192

show subpopulations

African (AFR)

AF:

0.381

AC:

15749

AN:

41332

American (AMR)

AF:

0.331

AC:

5048

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

996

AN:

3468

East Asian (EAS)

AF:

0.429

AC:

2212

AN:

5158

South Asian (SAS)

AF:

0.381

AC:

1835

AN:

4810

European-Finnish (FIN)

AF:

0.299

AC:

3154

AN:

10556

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.249

AC:

16881

AN:

67918

Other (OTH)

AF:

0.328

AC:

693

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1603

3207

4810

6414

8017

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.264

Hom.:

8623

Bravo

AF:

0.319

Asia WGS

AF:

0.414

AC:

1436

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.69

(source)

DANN

Benign

0.56

PhyloP100

-1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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