1-159295272-T-C

Position:

• chr1-159295272-T-C

Variant summary

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

The NM_002001.4(FCER1A):​c.-60+5519T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 151,956 control chromosomes in the GnomAD database, including 47,990 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 0.79 (47990 hom., cov: 30)
• Consequence: FCER1A NM_002001.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCER1A	NM_002001.4	c.-60+5519T>C		intron_variant			NP_001992.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCER1A	ENST00000368115.5	c.-60+5519T>C		intron_variant		1		ENSP00000357097.1

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119692 AN: 151838 Hom.: 47930 Cov.: 30

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.788 AC: 119812 AN: 151956 Hom.: 47990 Cov.: 30 AF XY: 0.786 AC XY: 58349 AN XY: 74256

Gnomad4 AFR AF: 0.934

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.762

Alfa AF: 0.750 Hom.: 19720

Bravo AF: 0.789

Asia WGS AF: 0.693 AC: 2410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.4
DANN	Benign	0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs2427824; hg19: chr1-159265062;