Variant chr1-161215268-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000490414.1(FCER1G):n.35G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,560,588 control chromosomes in the GnomAD database, including 69,147 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 0.32 ( 8190 hom., cov: 30)

Exomes 𝑓: 0.29 ( 60957 hom. )

Consequence

FCER1G
ENST00000490414.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.803

Variant links:

Genes affected

FCER1G (HGNC:3611): (Fc epsilon receptor Ig) The high affinity IgE receptor is a key molecule involved in allergic reactions. It is a tetramer composed of 1 alpha, 1 beta, and 2 gamma chains. The gamma chains are also subunits of other Fc receptors. [provided by RefSeq, Jul 2008]

FCER1G links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCER1G	NM_004106.2 linkuse as main transcript			upstream_gene_variant		ENST00000289902.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
FCER1G	ENST00000490414.1 linkuse as main transcript	n.35G>T	non_coding_transcript_exon_variant	1/4	2
FCER1G	ENST00000289902.2 linkuse as main transcript		upstream_gene_variant		1	NM_004106.2	P1
FCER1G	ENST00000367992.7 linkuse as main transcript		upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48650

AN:

151792

Hom.:

8177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.477

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.333

GnomAD4 exome

AF:

0.288

AC:

406293

AN:

1408678

Hom.:

60957

Cov.:

AF XY:

0.289

AC XY:

203750

AN XY:

704134

show subpopulations

Gnomad4 AFR exome

AF:

0.412

Gnomad4 AMR exome

AF:

0.383

Gnomad4 ASJ exome

AF:

0.287

Gnomad4 EAS exome

AF:

0.492

Gnomad4 SAS exome

AF:

0.372

Gnomad4 FIN exome

AF:

0.291

Gnomad4 NFE exome

AF:

0.265

Gnomad4 OTH exome

AF:

0.305

GnomAD4 genome

AF:

0.321

AC:

48709

AN:

151910

Hom.:

8190

Cov.:

AF XY:

0.324

AC XY:

24064

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.396

Gnomad4 AMR

AF:

0.338

Gnomad4 ASJ

AF:

0.294

Gnomad4 EAS

AF:

0.478

Gnomad4 SAS

AF:

0.394

Gnomad4 FIN

AF:

0.299

Gnomad4 NFE

AF:

0.259

Gnomad4 OTH

AF:

0.338

Alfa

AF:

0.283

Hom.:

1711

Bravo

AF:

0.333

Asia WGS

AF:

0.435

AC:

1510

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.82

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over