rs2277994

Variant names:

• chr19-7690632-A-C
• rs2277994
• NM_001220500.2:c.470-75T>G

Your query was ambiguous. Multiple possible variants found:

• chr19-7690632-A-C
• chr19-7690632-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002002.5(FCER2):​c.470-75T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FCER2 NM_002002.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 3 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002002.5. 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.470-75T>G		intron	N/A	NP_001207429.1
	FCER2	NM_002002.5		c.470-75T>G		intron	N/A	NP_001993.2
	FCER2	NM_001207019.3		c.467-75T>G		intron	N/A	NP_001193948.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCER2	ENST00000597921.6	TSL:1 MANE Select	c.470-75T>G		intron	N/A	ENSP00000471974.1
	FCER2	ENST00000346664.9	TSL:1	c.470-75T>G		intron	N/A	ENSP00000264072.6
	FCER2	ENST00000360067.8	TSL:5	c.467-75T>G		intron	N/A	ENSP00000353178.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1340220 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 662936

African (AFR) AF: 0.00 AC: 0 AN: 30870

American (AMR) AF: 0.00 AC: 0 AN: 37966

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22576

East Asian (EAS) AF: 0.00 AC: 0 AN: 37598

South Asian (SAS) AF: 0.00 AC: 0 AN: 75424

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40228

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4688

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1034824

Other (OTH) AF: 0.00 AC: 0 AN: 56046

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1068

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.016
DANN	Benign	0.44
PhyloP100		-2.2

Splicing

Name	Calibrated prediction	Score	Prediction
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: rs2277994; hg19: chr19-7755518;