rs11587213

Variant names:

• chr1-161215085-A-G
• rs11587213
• NM_004106.2:c.-237A>G

Variant summary

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

The NM_004106.2(FCER1G):​c.-237A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 430,190 control chromosomes in the GnomAD database, including 5,664 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 0.15 (1756 hom., cov: 30)
  • Exomes 𝑓: 0.15 (3908 hom.)
• Consequence: FCER1G NM_004106.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613

Genes affected

FCER1G (HGNC:3611): (Fc epsilon receptor Ig) The high affinity IgE receptor is a key molecule involved in allergic reactions. It is a tetramer composed of 1 alpha, 1 beta, and 2 gamma chains. The gamma chains are also subunits of other Fc receptors. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCER1G	NM_004106.2	c.-237A>G		upstream_gene_variant		ENST00000289902.2	NP_004097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER1G	ENST00000289902.2	c.-237A>G		upstream_gene_variant		1	NM_004106.2	ENSP00000289902.1
FCER1G	ENST00000367992.7	c.-237A>G		upstream_gene_variant		3		ENSP00000356971.3
FCER1G	ENST00000490414.1	n.-149A>G		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22187 AN: 151470 Hom.: 1748 Cov.: 30

Gnomad AFR AF: 0.0995

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0788

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.136

GnomAD4 exome AF: 0.149 AC: 41487 AN: 278620 Hom.: 3908 AF XY: 0.155 AC XY: 22699 AN XY: 146914

Gnomad4 AFR exome AF: 0.0836

Gnomad4 AMR exome AF: 0.115

Gnomad4 ASJ exome AF: 0.0985

Gnomad4 EAS exome AF: 0.0896

Gnomad4 SAS exome AF: 0.243

Gnomad4 FIN exome AF: 0.144

Gnomad4 NFE exome AF: 0.152

Gnomad4 OTH exome AF: 0.140

GnomAD4 genome AF: 0.147 AC: 22227 AN: 151570 Hom.: 1756 Cov.: 30 AF XY: 0.147 AC XY: 10922 AN XY: 74048

Gnomad4 AFR AF: 0.0998

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0786

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.136

Alfa AF: 0.170 Hom.: 3025

Bravo AF: 0.139

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11587213; hg19: chr1-161184875;