rs2070902

chr1-161217875-C-T

Variant summary

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

The NM_004106.2(FCER1G):c.50-111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 738,910 control chromosomes in the GnomAD database, including 33,241 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 0.31 (7602 hom., cov: 31)
  • Exomes 𝑓: 0.29 (25639 hom.)
• Consequence: FCER1G NM_004106.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCER1G	NM_004106.2	c.50-111C>T		intron_variant		ENST00000289902.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCER1G	ENST00000289902.2	c.50-111C>T		intron_variant		1	NM_004106.2	P1
FCER1G	ENST00000367992.7	c.50-111C>T		intron_variant		3
FCER1G	ENST00000490414.1	n.138-366C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46777 AN: 151706 Hom.: 7585 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.323

GnomAD4 exome AF: 0.287 AC: 168406 AN: 587086 Hom.: 25639 AF XY: 0.287 AC XY: 90206 AN XY: 314724

Gnomad4 AFR exome AF: 0.392

Gnomad4 AMR exome AF: 0.373

Gnomad4 ASJ exome AF: 0.279

Gnomad4 EAS exome AF: 0.450

Gnomad4 SAS exome AF: 0.357

Gnomad4 FIN exome AF: 0.286

Gnomad4 NFE exome AF: 0.244

Gnomad4 OTH exome AF: 0.294

GnomAD4 genome AF: 0.309 AC: 46840 AN: 151824 Hom.: 7602 Cov.: 31 AF XY: 0.312 AC XY: 23155 AN XY: 74192

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.328

Alfa AF: 0.262 Hom.: 7158

Bravo AF: 0.319

Asia WGS AF: 0.414 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.69
Dann	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2070902; hg19: chr1-161187665; COSMIC: COSV57154356; COSMIC: COSV57154356;