rs7548864

Variant names:

• chr1-159297465-G-A
• rs7548864
• ENST00000368115.5:c.-59-4841G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-159297465-G-A
• chr1-159297465-G-T

Variant summary

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

The ENST00000368115.5(FCER1A):​c.-59-4841G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,026 control chromosomes in the GnomAD database, including 2,913 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 0.16 (2913 hom., cov: 32)
• Consequence: FCER1A ENST00000368115.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.522 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
	FCER1A	NM_002001.4		c.-59-4841G>A		intron	N/A	NP_001992.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCER1A	ENST00000368115.5	TSL:1	c.-59-4841G>A		intron	N/A	ENSP00000357097.1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24843 AN: 151908 Hom.: 2911 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.164 AC: 24877 AN: 152026 Hom.: 2913 Cov.: 32 AF XY: 0.168 AC XY: 12462 AN XY: 74310

African (AFR) AF: 0.259 AC: 10731 AN: 41428

American (AMR) AF: 0.139 AC: 2127 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3470

East Asian (EAS) AF: 0.539 AC: 2779 AN: 5158

South Asian (SAS) AF: 0.278 AC: 1336 AN: 4814

European-Finnish (FIN) AF: 0.0938 AC: 993 AN: 10586

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5984 AN: 67990

Other (OTH) AF: 0.159 AC: 336 AN: 2112

Alfa AF: 0.116 Hom.: 4620

Bravo AF: 0.171

Asia WGS AF: 0.355 AC: 1231 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	0.037
DANN	Benign	0.23
PhyloP100		-1.4
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: rs7548864; hg19: chr1-159267255;