1-159296086-C-T

Variant names:

• chr1-159296086-C-T
• rs3845625
• ENST00000368115.5:c.-59-6220C>T

Variant summary

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

The NM_002001.4(FCER1A):​c.-59-6220C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,092 control chromosomes in the GnomAD database, including 1,586 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 0.13 (1586 hom., cov: 32)
• Consequence: FCER1A NM_002001.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 4 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 (AMR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002001.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCER1A	NM_002001.4		c.-59-6220C>T		intron	N/A	NP_001992.1	P12319

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCER1A	ENST00000368115.5	TSL:1	c.-59-6220C>T		intron	N/A	ENSP00000357097.1	P12319

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19377 AN: 151974 Hom.: 1586 Cov.: 32

Gnomad AFR AF: 0.0380

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.127 AC: 19377 AN: 152092 Hom.: 1586 Cov.: 32 AF XY: 0.131 AC XY: 9773 AN XY: 74350

African (AFR) AF: 0.0380 AC: 1576 AN: 41516

American (AMR) AF: 0.171 AC: 2617 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3468

East Asian (EAS) AF: 0.0158 AC: 82 AN: 5192

South Asian (SAS) AF: 0.108 AC: 518 AN: 4816

European-Finnish (FIN) AF: 0.228 AC: 2412 AN: 10566

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11344 AN: 67962

Other (OTH) AF: 0.123 AC: 260 AN: 2106

Alfa AF: 0.0755 Hom.: 127

Bravo AF: 0.118

Asia WGS AF: 0.0610 AC: 213 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.58
DANN	Benign	0.19
PhyloP100		-0.84
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: rs3845625; hg19: chr1-159265876;