1-159288755-G-A

Position:

• chr1-159288755-G-A

Variant summary

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

The NM_002001.4(FCER1A):​c.-97-961G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,010 control chromosomes in the GnomAD database, including 3,856 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 0.20 (3856 hom., cov: 32)
• Consequence: FCER1A NM_002001.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCER1A	NM_002001.4	c.-97-961G>A		intron_variant			NP_001992.1
		n.159288755G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30848 AN: 151892 Hom.: 3856 Cov.: 32

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.203 AC: 30848 AN: 152010 Hom.: 3856 Cov.: 32 AF XY: 0.201 AC XY: 14967 AN XY: 74288

Gnomad4 AFR AF: 0.0861

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0473

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.208

Alfa AF: 0.255 Hom.: 5071

Bravo AF: 0.185

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2427837; hg19: chr1-159258545;