rs2070902
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004106.2(FCER1G):c.50-111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 738,910 control chromosomes in the GnomAD database, including 33,241 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 0.31 ( 7602 hom., cov: 31)
Exomes 𝑓: 0.29 ( 25639 hom. )
Consequence
FCER1G
NM_004106.2 intron
NM_004106.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.05
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]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCER1G | NM_004106.2 | c.50-111C>T | intron_variant | ENST00000289902.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCER1G | ENST00000289902.2 | c.50-111C>T | intron_variant | 1 | NM_004106.2 | P1 | |||
FCER1G | ENST00000367992.7 | c.50-111C>T | intron_variant | 3 | |||||
FCER1G | ENST00000490414.1 | n.138-366C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.308 AC: 46777AN: 151706Hom.: 7585 Cov.: 31
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GnomAD4 exome AF: 0.287 AC: 168406AN: 587086Hom.: 25639 AF XY: 0.287 AC XY: 90206AN XY: 314724
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GnomAD4 genome ? AF: 0.309 AC: 46840AN: 151824Hom.: 7602 Cov.: 31 AF XY: 0.312 AC XY: 23155AN XY: 74192
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at