1-161215268-G-T

Variant names:

• chr1-161215268-G-T
• rs2070901
• ENST00000490414.1:n.35G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000490414.1(FCER1G):​n.35G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,560,588 control chromosomes in the GnomAD database, including 69,147 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 0.32 (8190 hom., cov: 30)
  • Exomes 𝑓: 0.29 (60957 hom.)
• Consequence: FCER1G ENST00000490414.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 46 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000490414.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCER1G	NM_004106.2	MANE Select	c.-54G>T		upstream_gene	N/A	NP_004097.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCER1G	ENST00000490414.1	TSL:2	n.35G>T		non_coding_transcript_exon	Exon 1 of 4
	FCER1G	ENST00000289902.2	TSL:1 MANE Select	c.-54G>T		upstream_gene	N/A	ENSP00000289902.1
	FCER1G	ENST00000367992.7	TSL:3	c.-54G>T		upstream_gene	N/A	ENSP00000356971.3

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48650 AN: 151792 Hom.: 8177 Cov.: 30

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.288 AC: 406293 AN: 1408678 Hom.: 60957 Cov.: 22 AF XY: 0.289 AC XY: 203750 AN XY: 704134

African (AFR) AF: 0.412 AC: 13379 AN: 32442

American (AMR) AF: 0.383 AC: 17092 AN: 44596

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 7373 AN: 25728

East Asian (EAS) AF: 0.492 AC: 19357 AN: 39326

South Asian (SAS) AF: 0.372 AC: 31664 AN: 85202

European-Finnish (FIN) AF: 0.291 AC: 15486 AN: 53186

Middle Eastern (MID) AF: 0.313 AC: 1751 AN: 5594

European-Non Finnish (NFE) AF: 0.265 AC: 282353 AN: 1064200

Other (OTH) AF: 0.305 AC: 17838 AN: 58404

GnomAD4 genome AF: 0.321 AC: 48709 AN: 151910 Hom.: 8190 Cov.: 30 AF XY: 0.324 AC XY: 24064 AN XY: 74242

African (AFR) AF: 0.396 AC: 16407 AN: 41404

American (AMR) AF: 0.338 AC: 5163 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2448 AN: 5126

South Asian (SAS) AF: 0.394 AC: 1895 AN: 4804

European-Finnish (FIN) AF: 0.299 AC: 3158 AN: 10554

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17603 AN: 67970

Other (OTH) AF: 0.338 AC: 713 AN: 2110

Alfa AF: 0.297 Hom.: 3634

Bravo AF: 0.333

Asia WGS AF: 0.435 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		0.80
PromoterAI		-0.051	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2070901; hg19: chr1-161185058; COSMIC: COSV57154349;