rs2494250

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-159308461-G-C
• chr1-159308461-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER1A	ENST00000368115.5	c.*529G>C		downstream_gene_variant		1		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

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.748

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2494250; hg19: chr1-159278251;