19-7690696-A-G

Position:

• chr19-7690696-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001220500.2(FCER2):​c.470-139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 777,092 control chromosomes in the GnomAD database, including 34,473 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 (10191 hom., cov: 32)
  • Exomes 𝑓: 0.27 (24282 hom.)
• Consequence: FCER2 NM_001220500.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCER2	NM_001220500.2	c.470-139T>C		intron_variant		ENST00000597921.6
FCER2	NM_001207019.3	c.467-139T>C		intron_variant
FCER2	NM_002002.5	c.470-139T>C		intron_variant
FCER2	XM_005272462.5	c.470-139T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCER2	ENST00000597921.6	c.470-139T>C		intron_variant		1	NM_001220500.2	P2

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52577 AN: 151754 Hom.: 10172 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.344

GnomAD4 exome AF: 0.268 AC: 167550 AN: 625220 Hom.: 24282 AF XY: 0.273 AC XY: 87752 AN XY: 321816

Gnomad4 AFR exome AF: 0.506

Gnomad4 AMR exome AF: 0.183

Gnomad4 ASJ exome AF: 0.315

Gnomad4 EAS exome AF: 0.280

Gnomad4 SAS exome AF: 0.349

Gnomad4 FIN exome AF: 0.234

Gnomad4 NFE exome AF: 0.252

Gnomad4 OTH exome AF: 0.296

GnomAD4 genome AF: 0.347 AC: 52627 AN: 151872 Hom.: 10191 Cov.: 32 AF XY: 0.343 AC XY: 25481 AN XY: 74250

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.339

Alfa AF: 0.319 Hom.: 1063

Bravo AF: 0.352

Asia WGS AF: 0.344 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2277992; hg19: chr19-7755582;