chr1-159308461-G-C

Variant names:

• chr1-159308461-G-C
• rs2494250
• ENST00000368115.5:c.*529G>C

Variant summary

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

The ENST00000368115.5(FCER1A):​c.*529G>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,108 control chromosomes in the GnomAD database, including 46,670 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 0.78 (46670 hom., cov: 31)
• Consequence: FCER1A ENST00000368115.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 17 publications found

Genes affected

FCER1A (HGNC:3609): (Fc epsilon receptor Ia) The immunoglobulin epsilon receptor (IgE receptor) is the initiator of the allergic response. When two or more high-affinity IgE receptors are brought together by allergen-bound IgE molecules, mediators such as histamine that are responsible for allergy symptoms are released. This receptor is comprised of an alpha subunit, a beta subunit, and two gamma subunits. The protein encoded by this gene represents the alpha subunit. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368115.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCER1A	ENST00000368115.5	TSL:1	c.*529G>C		downstream_gene	N/A	ENSP00000357097.1

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117907 AN: 151990 Hom.: 46620 Cov.: 31

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.753

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.776 AC: 118017 AN: 152108 Hom.: 46670 Cov.: 31 AF XY: 0.772 AC XY: 57384 AN XY: 74354

African (AFR) AF: 0.932 AC: 38685 AN: 41526

American (AMR) AF: 0.699 AC: 10673 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2139 AN: 3472

East Asian (EAS) AF: 0.760 AC: 3916 AN: 5156

South Asian (SAS) AF: 0.581 AC: 2796 AN: 4814

European-Finnish (FIN) AF: 0.765 AC: 8079 AN: 10558

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49363 AN: 67994

Other (OTH) AF: 0.748 AC: 1581 AN: 2114

Alfa AF: 0.711 Hom.: 18834

Bravo AF: 0.778

Asia WGS AF: 0.613 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.36
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2494250; hg19: chr1-159278251;