rs7249320

Positions:

• chr19-7698159-C-A
• chr19-7698159-C-T

Variant summary

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

The NM_001220500.2(FCER2):​c.190+197G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,064 control chromosomes in the GnomAD database, including 7,086 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 0.29 (7086 hom., cov: 31)
• Consequence: FCER2 NM_001220500.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCER2	NM_001220500.2	c.190+197G>T		intron_variant		ENST00000597921.6
FCER2	NM_001207019.3	c.187+197G>T		intron_variant
FCER2	NM_002002.5	c.190+197G>T		intron_variant
FCER2	XM_005272462.5	c.190+197G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCER2	ENST00000597921.6	c.190+197G>T		intron_variant		1	NM_001220500.2	P2

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44016 AN: 151946 Hom.: 7077 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.283

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.290 AC: 44056 AN: 152064 Hom.: 7086 Cov.: 31 AF XY: 0.287 AC XY: 21345 AN XY: 74322

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.279

Alfa AF: 0.177 Hom.: 533

Bravo AF: 0.294

Asia WGS AF: 0.252 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.97
DANN	Benign	0.49

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: rs7249320; hg19: chr19-7763045;