rs2287867

Variant names:

• chr19-7699855-G-A
• rs2287867
• NM_001220500.2:c.-85-10C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-7699855-G-A
• chr19-7699855-G-C
• chr19-7699855-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001220500.2(FCER2):​c.-85-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 1,221,064 control chromosomes in the GnomAD database, including 179,865 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 0.50 (19861 hom., cov: 31)
  • Exomes 𝑓: 0.55 (160004 hom.)
• Consequence: FCER2 NM_001220500.2 intron
• Scores: Splicing: ADA: 0.0003733
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• Publications: 9 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCER2	NM_001220500.2	c.-85-10C>T		intron_variant	Intron 1 of 10	ENST00000597921.6	NP_001207429.1
FCER2	NM_002002.5	c.-85-10C>T		intron_variant	Intron 1 of 10		NP_001993.2
FCER2	XM_005272462.5	c.-81-14C>T		intron_variant	Intron 1 of 10		XP_005272519.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER2	ENST00000597921.6	c.-85-10C>T		intron_variant	Intron 1 of 10	1	NM_001220500.2	ENSP00000471974.1

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76487 AN: 151880 Hom.: 19835 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.526

GnomAD4 exome AF: 0.546 AC: 583610 AN: 1069066 Hom.: 160004 Cov.: 14 AF XY: 0.548 AC XY: 299545 AN XY: 546256

African (AFR) AF: 0.376 AC: 9662 AN: 25704

American (AMR) AF: 0.527 AC: 20639 AN: 39180

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 13788 AN: 23328

East Asian (EAS) AF: 0.667 AC: 24954 AN: 37386

South Asian (SAS) AF: 0.577 AC: 43854 AN: 76062

European-Finnish (FIN) AF: 0.584 AC: 30104 AN: 51514

Middle Eastern (MID) AF: 0.558 AC: 2766 AN: 4960

European-Non Finnish (NFE) AF: 0.540 AC: 412163 AN: 763432

Other (OTH) AF: 0.541 AC: 25680 AN: 47500

GnomAD4 genome AF: 0.504 AC: 76555 AN: 151998 Hom.: 19861 Cov.: 31 AF XY: 0.507 AC XY: 37681 AN XY: 74282

African (AFR) AF: 0.376 AC: 15595 AN: 41448

American (AMR) AF: 0.531 AC: 8116 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2026 AN: 3470

East Asian (EAS) AF: 0.645 AC: 3318 AN: 5142

South Asian (SAS) AF: 0.581 AC: 2798 AN: 4816

European-Finnish (FIN) AF: 0.583 AC: 6158 AN: 10556

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36915 AN: 67984

Other (OTH) AF: 0.530 AC: 1116 AN: 2104

Alfa AF: 0.535 Hom.: 12756

Bravo AF: 0.492

Asia WGS AF: 0.630 AC: 2189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	16
DANN	Benign	0.71
PhyloP100		2.0
PromoterAI		-0.0066	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00037
dbscSNV1_RF	Benign	0.052
SpliceAI score (max)		0.030		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: rs2287867; hg19: chr19-7764741; COSMIC: COSV107410276; COSMIC: COSV107410276;