rs3214456

Positions:

• chr19-7699659-G-GC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001220500.2(FCER2):​c.22+79_22+80insG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.63 (30553 hom., cov: 0)
  • Exomes 𝑓: 0.65 (262362 hom.)
• Consequence: FCER2 NM_001220500.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCER2	NM_001220500.2	c.22+79_22+80insG		intron_variant		ENST00000597921.6
FCER2	NM_002002.5	c.22+79_22+80insG		intron_variant
FCER2	XM_005272462.5	c.22+79_22+80insG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCER2	ENST00000597921.6	c.22+79_22+80insG		intron_variant		1	NM_001220500.2	P2

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95496 AN: 151156 Hom.: 30518 Cov.: 0

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.646

GnomAD4 exome AF: 0.645 AC: 801699 AN: 1242430 Hom.: 262362 Cov.: 19 AF XY: 0.649 AC XY: 408387 AN XY: 629282

Gnomad4 AFR exome AF: 0.554

Gnomad4 AMR exome AF: 0.641

Gnomad4 ASJ exome AF: 0.695

Gnomad4 EAS exome AF: 0.842

Gnomad4 SAS exome AF: 0.736

Gnomad4 FIN exome AF: 0.675

Gnomad4 NFE exome AF: 0.628

Gnomad4 OTH exome AF: 0.653

GnomAD4 genome AF: 0.632 AC: 95592 AN: 151274 Hom.: 30553 Cov.: 0 AF XY: 0.636 AC XY: 46960 AN XY: 73876

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.648

Alfa AF: 0.637 Hom.: 3816

Bravo AF: 0.623

Asia WGS AF: 0.790 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs3214456; hg19: chr19-7764545;