rs3557

Variant names:

• chr1-161219103-T-G
• rs3557
• NM_004106.2:c.*160T>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.*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
• Publications: 32 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=-0.78).
• 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 rank	MANE	Protein	UniProt
FCER1G	NM_004106.2	c.*160T>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000289902.2	NP_004097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER1G	ENST00000289902.2	c.*160T>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_004106.2	ENSP00000289902.1
FCER1G	ENST00000490414.1	n.417T>G		non_coding_transcript_exon_variant	Exon 4 of 4	2
FCER1G	ENST00000367992.7	c.198+380T>G		intron_variant	Intron 4 of 4	3		ENSP00000356971.3

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

African (AFR) AF: 0.0449 AC: 575 AN: 12810

American (AMR) AF: 0.0436 AC: 866 AN: 19870

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 1115 AN: 14060

East Asian (EAS) AF: 0.00592 AC: 186 AN: 31410

South Asian (SAS) AF: 0.0875 AC: 4145 AN: 47352

European-Finnish (FIN) AF: 0.0522 AC: 2161 AN: 41422

Middle Eastern (MID) AF: 0.0498 AC: 165 AN: 3314

European-Non Finnish (NFE) AF: 0.0852 AC: 23603 AN: 277106

Other (OTH) AF: 0.0721 AC: 1930 AN: 26770

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

African (AFR) AF: 0.0447 AC: 1857 AN: 41554

American (AMR) AF: 0.0448 AC: 684 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3472

East Asian (EAS) AF: 0.00656 AC: 34 AN: 5184

South Asian (SAS) AF: 0.0894 AC: 431 AN: 4822

European-Finnish (FIN) AF: 0.0464 AC: 492 AN: 10604

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0860 AC: 5849 AN: 68028

Other (OTH) AF: 0.0634 AC: 134 AN: 2114

Alfa AF: 0.0791 Hom.: 1485

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
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3557; hg19: chr1-161188893;