rs3214456

Variant names:

• chr19-7699659-G-GC
• rs3214456
• NM_001220500.2:c.22+79dupG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001220500.2(FCER2):​c.22+79dupG 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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FCER2	NM_001220500.2	c.22+79dupG		intron_variant	Intron 2 of 10	ENST00000597921.6	NP_001207429.1
FCER2	NM_002002.5	c.22+79dupG		intron_variant	Intron 2 of 10		NP_001993.2
FCER2	XM_005272462.5	c.22+79dupG		intron_variant	Intron 2 of 10		XP_005272519.1
FCER2	NM_001207019.3	c.-265dupG		upstream_gene_variant			NP_001193948.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER2	ENST00000597921.6	c.22+79_22+80insG		intron_variant	Intron 2 of 10	1	NM_001220500.2	ENSP00000471974.1

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

African (AFR) AF: 0.554 AC: 16085 AN: 29050

American (AMR) AF: 0.641 AC: 28425 AN: 44346

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 17165 AN: 24688

East Asian (EAS) AF: 0.842 AC: 32634 AN: 38738

South Asian (SAS) AF: 0.736 AC: 60165 AN: 81724

European-Finnish (FIN) AF: 0.675 AC: 35962 AN: 53248

Middle Eastern (MID) AF: 0.668 AC: 3440 AN: 5150

European-Non Finnish (NFE) AF: 0.628 AC: 573065 AN: 912264

Other (OTH) AF: 0.653 AC: 34758 AN: 53222

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

African (AFR) AF: 0.562 AC: 23119 AN: 41120

American (AMR) AF: 0.661 AC: 10031 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2381 AN: 3470

East Asian (EAS) AF: 0.835 AC: 4246 AN: 5082

South Asian (SAS) AF: 0.738 AC: 3545 AN: 4804

European-Finnish (FIN) AF: 0.671 AC: 6998 AN: 10424

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43329 AN: 67878

Other (OTH) AF: 0.648 AC: 1364 AN: 2106

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

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3214456; hg19: chr19-7764545;