rs2494262

Positions:

• chr1-159283882-C-A
• chr1-159283882-C-G
• chr1-159283882-C-T

Variant summary

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

The NM_002001.4(FCER1A):​c.-112C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,954 control chromosomes in the GnomAD database, including 15,216 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 0.41 (15216 hom., cov: 31)
• Consequence: FCER1A NM_002001.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

FCER1A (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 (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCER1A	NM_002001.4	c.-112C>A		5_prime_UTR_variant	1/7		NP_001992.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62130 AN: 151836 Hom.: 15217 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.409 AC: 62143 AN: 151954 Hom.: 15216 Cov.: 31 AF XY: 0.410 AC XY: 30443 AN XY: 74260

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.439

Alfa AF: 0.487 Hom.: 17595

Bravo AF: 0.391

Asia WGS AF: 0.520 AC: 1808 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	4.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2494262; hg19: chr1-159253672;