1-159302021-T-C

Variant names:

• chr1-159302021-T-C
• rs2427827
• ENST00000368115.5:c.-59-285T>C

Variant summary

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

The ENST00000368115.5(FCER1A):​c.-59-285T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,104 control chromosomes in the GnomAD database, including 34,046 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 0.65 (34046 hom., cov: 32)
• Consequence: FCER1A ENST00000368115.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 33 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCER1A	NM_002001.4	c.-59-285T>C		intron_variant	Intron 2 of 6		NP_001992.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER1A	ENST00000368115.5	c.-59-285T>C		intron_variant	Intron 1 of 5	1		ENSP00000357097.1

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98701 AN: 151986 Hom.: 34005 Cov.: 32

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.650 AC: 98794 AN: 152104 Hom.: 34046 Cov.: 32 AF XY: 0.641 AC XY: 47691 AN XY: 74384

African (AFR) AF: 0.892 AC: 37055 AN: 41530

American (AMR) AF: 0.529 AC: 8095 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1748 AN: 3472

East Asian (EAS) AF: 0.742 AC: 3830 AN: 5164

South Asian (SAS) AF: 0.477 AC: 2297 AN: 4820

European-Finnish (FIN) AF: 0.537 AC: 5671 AN: 10558

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.562 AC: 38163 AN: 67958

Other (OTH) AF: 0.625 AC: 1319 AN: 2110

Alfa AF: 0.605 Hom.: 44514

Bravo AF: 0.662

Asia WGS AF: 0.545 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.76
PhyloP100		-0.083
PromoterAI		0.0075	Neutral
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: rs2427827; hg19: chr1-159271811;