Variant rs28364072 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001220500.2(FCER2):c.621+7T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,612,512 control chromosomes in the GnomAD database, including 72,921 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.35 ( 10842 hom., cov: 32)

Exomes 𝑓: 0.29 ( 62079 hom. )

Consequence

FCER2
NM_001220500.2 splice_region, intron

Scores

Splicing: ADA: 0.0001808

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.167

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
FCER2	NM_001220500.2 linkuse as main transcript	c.621+7T>C	splice_region_variant, intron_variant	ENST00000597921.6
FCER2	NM_001207019.3 linkuse as main transcript	c.618+7T>C	splice_region_variant, intron_variant
FCER2	NM_002002.5 linkuse as main transcript	c.621+7T>C	splice_region_variant, intron_variant
FCER2	XM_005272462.5 linkuse as main transcript	c.621+7T>C	splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCER2	ENST00000597921.6 linkuse as main transcript	c.621+7T>C		splice_region_variant, intron_variant		1	NM_001220500.2	P2

Frequencies

GnomAD3 genomes

AF:

0.354

AC:

53755

AN:

151856

Hom.:

10814

Cov.:

show subpopulations

Gnomad AFR

AF:

0.551

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.342

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.372

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.352

GnomAD3 exomes

AF:

0.293

AC:

73199

AN:

250108

Hom.:

11951

AF XY:

0.296

AC XY:

39967

AN XY:

135184

show subpopulations

Gnomad AFR exome

AF:

0.561

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.296

Gnomad EAS exome

AF:

0.368

Gnomad SAS exome

AF:

0.361

Gnomad FIN exome

AF:

0.228

Gnomad NFE exome

AF:

0.277

Gnomad OTH exome

AF:

0.279

GnomAD4 exome

AF:

0.286

AC:

417076

AN:

1460538

Hom.:

62079

Cov.:

AF XY:

0.288

AC XY:

209081

AN XY:

726458

show subpopulations

Gnomad4 AFR exome

AF:

0.569

Gnomad4 AMR exome

AF:

0.169

Gnomad4 ASJ exome

AF:

0.301

Gnomad4 EAS exome

AF:

0.295

Gnomad4 SAS exome

AF:

0.355

Gnomad4 FIN exome

AF:

0.231

Gnomad4 NFE exome

AF:

0.277

Gnomad4 OTH exome

AF:

0.308

GnomAD4 genome

AF:

0.354

AC:

53815

AN:

151974

Hom.:

10842

Cov.:

AF XY:

0.351

AC XY:

26061

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.552

Gnomad4 AMR

AF:

0.253

Gnomad4 ASJ

AF:

0.300

Gnomad4 EAS

AF:

0.343

Gnomad4 SAS

AF:

0.369

Gnomad4 FIN

AF:

0.233

Gnomad4 NFE

AF:

0.278

Gnomad4 OTH

AF:

0.346

Alfa

AF:

0.287

Hom.:

2865

Bravo

AF:

0.361

Asia WGS

AF:

0.343

AC:

1191

AN:

3478

EpiCase

AF:

0.278

EpiControl

AF:

0.279

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.3

DANN

Benign

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00018

dbscSNV1_RF

Benign

0.0020

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over