chr1-161215085-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 36 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0836 AC: 682 AN: 8154

American (AMR) AF: 0.115 AC: 1469 AN: 12748

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 874 AN: 8870

East Asian (EAS) AF: 0.0896 AC: 1865 AN: 20804

South Asian (SAS) AF: 0.243 AC: 6119 AN: 25142

European-Finnish (FIN) AF: 0.144 AC: 2803 AN: 19424

Middle Eastern (MID) AF: 0.135 AC: 167 AN: 1240

European-Non Finnish (NFE) AF: 0.152 AC: 25219 AN: 165832

Other (OTH) AF: 0.140 AC: 2289 AN: 16406

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

African (AFR) AF: 0.0998 AC: 4122 AN: 41282

American (AMR) AF: 0.132 AC: 2003 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3468

East Asian (EAS) AF: 0.0786 AC: 404 AN: 5138

South Asian (SAS) AF: 0.254 AC: 1218 AN: 4796

European-Finnish (FIN) AF: 0.156 AC: 1627 AN: 10442

Middle Eastern (MID) AF: 0.131 AC: 38 AN: 290

European-Non Finnish (NFE) AF: 0.176 AC: 11955 AN: 67920

Other (OTH) AF: 0.136 AC: 286 AN: 2108

Alfa AF: 0.165 Hom.: 7200

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
PhyloP100		0.61
PromoterAI		-0.024	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11587213; hg19: chr1-161184875;