rs2277993

Variant names:

• chr19-7690685-G-A
• rs2277993
• NM_001220500.2:c.470-128C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-7690685-G-A
• chr19-7690685-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.470-128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 871,008 control chromosomes in the GnomAD database, including 38,400 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 (10423 hom., cov: 32)
  • Exomes 𝑓: 0.27 (27977 hom.)
• Consequence: FCER2 NM_001220500.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001220500.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCER2	NM_001220500.2	MANE Select	c.470-128C>T		intron	N/A	NP_001207429.1	P06734
	FCER2	NM_002002.5		c.470-128C>T		intron	N/A	NP_001993.2
	FCER2	NM_001207019.3		c.467-128C>T		intron	N/A	NP_001193948.2	K3W4U1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCER2	ENST00000597921.6	TSL:1 MANE Select	c.470-128C>T		intron	N/A	ENSP00000471974.1	P06734
	FCER2	ENST00000346664.9	TSL:1	c.470-128C>T		intron	N/A	ENSP00000264072.6	P06734
	FCER2	ENST00000360067.8	TSL:5	c.467-128C>T		intron	N/A	ENSP00000353178.4	K3W4U1

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53061 AN: 151740 Hom.: 10402 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.349

GnomAD4 exome AF: 0.270 AC: 194033 AN: 719150 Hom.: 27977 AF XY: 0.275 AC XY: 101130 AN XY: 367470

African (AFR) AF: 0.522 AC: 9036 AN: 17314

American (AMR) AF: 0.193 AC: 4761 AN: 24606

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 5181 AN: 16220

East Asian (EAS) AF: 0.282 AC: 9120 AN: 32374

South Asian (SAS) AF: 0.357 AC: 19743 AN: 55262

European-Finnish (FIN) AF: 0.236 AC: 7500 AN: 31788

Middle Eastern (MID) AF: 0.349 AC: 912 AN: 2612

European-Non Finnish (NFE) AF: 0.253 AC: 127321 AN: 504034

Other (OTH) AF: 0.299 AC: 10459 AN: 34940

GnomAD4 genome AF: 0.350 AC: 53112 AN: 151858 Hom.: 10423 Cov.: 32 AF XY: 0.346 AC XY: 25698 AN XY: 74202

African (AFR) AF: 0.528 AC: 21853 AN: 41376

American (AMR) AF: 0.254 AC: 3879 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1770 AN: 5142

South Asian (SAS) AF: 0.377 AC: 1814 AN: 4814

European-Finnish (FIN) AF: 0.234 AC: 2480 AN: 10582

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19060 AN: 67908

Other (OTH) AF: 0.344 AC: 724 AN: 2104

Alfa AF: 0.183 Hom.: 406

Bravo AF: 0.356

Asia WGS AF: 0.346 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		-0.28
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2277993;

hg19: chr19-7755571;