rs3557

chr1-161219103-T-G

Variant summary

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

The NM_004106.2(FCER1G):c.*160T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 626,370 control chromosomes in the GnomAD database, including 1,826 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 0.065 (364 hom., cov: 32)
  • Exomes 𝑓: 0.073 (1462 hom.)
• Consequence: FCER1G NM_004106.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCER1G	NM_004106.2	c.*160T>G		3_prime_UTR_variant	5/5	ENST00000289902.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCER1G	ENST00000289902.2	c.*160T>G		3_prime_UTR_variant	5/5	1	NM_004106.2	P1
FCER1G	ENST00000367992.7	c.198+380T>G		intron_variant		3
FCER1G	ENST00000490414.1	n.417T>G		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.0647 AC: 9846 AN: 152138 Hom.: 364 Cov.: 32

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.0889

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.0636

GnomAD4 exome AF: 0.0733 AC: 34746 AN: 474114 Hom.: 1462 Cov.: 4 AF XY: 0.0740 AC XY: 18568 AN XY: 250822

Gnomad4 AFR exome AF: 0.0449

Gnomad4 AMR exome AF: 0.0436

Gnomad4 ASJ exome AF: 0.0793

Gnomad4 EAS exome AF: 0.00592

Gnomad4 SAS exome AF: 0.0875

Gnomad4 FIN exome AF: 0.0522

Gnomad4 NFE exome AF: 0.0852

Gnomad4 OTH exome AF: 0.0721

GnomAD4 genome AF: 0.0647 AC: 9846 AN: 152256 Hom.: 364 Cov.: 32 AF XY: 0.0623 AC XY: 4641 AN XY: 74452

Gnomad4 AFR AF: 0.0447

Gnomad4 AMR AF: 0.0448

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.00656

Gnomad4 SAS AF: 0.0894

Gnomad4 FIN AF: 0.0464

Gnomad4 NFE AF: 0.0860

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0802 Hom.: 576

Bravo AF: 0.0633

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	3.3
Dann	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs3557; hg19: chr1-161188893;