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GeneBe

rs2277993

Variant summary

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

The NM_001220500.2(FCER2):​c.470-128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 871,008 control chromosomes in the GnomAD database, including 38,400 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 0.35 ( 10423 hom., cov: 32)
Exomes 𝑓: 0.27 ( 27977 hom. )

Consequence

FCER2
NM_001220500.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.281
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]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FCER2NM_001220500.2 linkuse as main transcriptc.470-128C>T intron_variant ENST00000597921.6
FCER2NM_001207019.3 linkuse as main transcriptc.467-128C>T intron_variant
FCER2NM_002002.5 linkuse as main transcriptc.470-128C>T intron_variant
FCER2XM_005272462.5 linkuse as main transcriptc.470-128C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FCER2ENST00000597921.6 linkuse as main transcriptc.470-128C>T intron_variant 1 NM_001220500.2 P2

Frequencies

GnomAD3 genomes
AF:
0.350
AC:
53061
AN:
151740
Hom.:
10402
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.528
Gnomad AMI
AF:
0.349
Gnomad AMR
AF:
0.255
Gnomad ASJ
AF:
0.318
Gnomad EAS
AF:
0.344
Gnomad SAS
AF:
0.378
Gnomad FIN
AF:
0.234
Gnomad MID
AF:
0.386
Gnomad NFE
AF:
0.281
Gnomad OTH
AF:
0.349
GnomAD4 exome
AF:
0.270
AC:
194033
AN:
719150
Hom.:
27977
AF XY:
0.275
AC XY:
101130
AN XY:
367470
show subpopulations
Gnomad4 AFR exome
AF:
0.522
Gnomad4 AMR exome
AF:
0.193
Gnomad4 ASJ exome
AF:
0.319
Gnomad4 EAS exome
AF:
0.282
Gnomad4 SAS exome
AF:
0.357
Gnomad4 FIN exome
AF:
0.236
Gnomad4 NFE exome
AF:
0.253
Gnomad4 OTH exome
AF:
0.299
GnomAD4 genome
AF:
0.350
AC:
53112
AN:
151858
Hom.:
10423
Cov.:
32
AF XY:
0.346
AC XY:
25698
AN XY:
74202
show subpopulations
Gnomad4 AFR
AF:
0.528
Gnomad4 AMR
AF:
0.254
Gnomad4 ASJ
AF:
0.318
Gnomad4 EAS
AF:
0.344
Gnomad4 SAS
AF:
0.377
Gnomad4 FIN
AF:
0.234
Gnomad4 NFE
AF:
0.281
Gnomad4 OTH
AF:
0.344
Alfa
AF:
0.161
Hom.:
301
Bravo
AF:
0.356
Asia WGS
AF:
0.346
AC:
1200
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
2.4
DANN
Benign
0.57

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.

Other links and lift over

dbSNP: rs2277993; hg19: chr19-7755571; API