rs747524495

Variant names:

• chr19-7690243-C-A
• rs747524495
• NM_001220500.2:c.644G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-7690243-C-A
• chr19-7690243-C-G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001220500.2(FCER2):​c.644G>T​(p.Ser215Ile) variant causes a missense 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. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S215T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FCER2 NM_001220500.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.18450812).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCER2	NM_001220500.2	c.644G>T	p.Ser215Ile	missense_variant	Exon 10 of 11	ENST00000597921.6	NP_001207429.1
FCER2	NM_002002.5	c.644G>T	p.Ser215Ile	missense_variant	Exon 10 of 11		NP_001993.2
FCER2	NM_001207019.3	c.641G>T	p.Ser214Ile	missense_variant	Exon 9 of 10		NP_001193948.2
FCER2	XM_005272462.5	c.644G>T	p.Ser215Ile	missense_variant	Exon 10 of 11		XP_005272519.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER2	ENST00000597921.6	c.644G>T	p.Ser215Ile	missense_variant	Exon 10 of 11	1	NM_001220500.2	ENSP00000471974.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.70
DEOGEN2	Benign	0.16	.;T;T
Eigen	Benign	-0.70
Eigen_PC	Benign	-0.91
FATHMM_MKL	Benign	0.061	N
LIST_S2	Benign	0.36	T;.;T
M_CAP	Benign	0.0037	T
MetaRNN	Benign	0.18	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.7	.;L;L
PhyloP100		-0.28
PrimateAI	Benign	0.36	T
PROVEAN	Uncertain	-3.0	D;D;.
REVEL	Benign	0.054
Sift	Uncertain	0.0010	D;D;.
Sift4G	Benign	0.071	T;T;T
Polyphen		0.96	.;D;D
Vest4		0.18
MutPred		0.55		.;Loss of disorder (P = 0.0053);Loss of disorder (P = 0.0053);
MVP		0.50
MPC		0.11
ClinPred		0.63	D
GERP RS		0.089
Varity_R		0.32
gMVP		0.48
Mutation Taster		=90/10	polymorphism

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

Other links and lift over

dbSNP: rs747524495; hg19: chr19-7755129;