1-159307882-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001387280.1(FCER1A):c.724G>T(p.Gly242Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,613,372 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G242A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001387280.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCER1A | NM_001387280.1 | c.724G>T | p.Gly242Cys | missense_variant | 5/5 | ENST00000693622.1 | |
FCER1A | NM_002001.4 | c.724G>T | p.Gly242Cys | missense_variant | 7/7 | ||
FCER1A | NM_001387282.1 | c.625G>T | p.Gly209Cys | missense_variant | 5/5 | ||
FCER1A | NM_001387281.1 | c.469G>T | p.Gly157Cys | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCER1A | ENST00000693622.1 | c.724G>T | p.Gly242Cys | missense_variant | 5/5 | NM_001387280.1 | P1 | ||
FCER1A | ENST00000368115.5 | c.724G>T | p.Gly242Cys | missense_variant | 6/6 | 1 | P1 | ||
FCER1A | ENST00000368114.1 | c.625G>T | p.Gly209Cys | missense_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250966Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135622
GnomAD4 exome AF: 0.0000329 AC: 48AN: 1461086Hom.: 1 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 726794
GnomAD4 genome AF: 0.000420 AC: 64AN: 152286Hom.: 1 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2021 | The c.724G>T (p.G242C) alteration is located in exon 7 (coding exon 5) of the FCER1A gene. This alteration results from a G to T substitution at nucleotide position 724, causing the glycine (G) at amino acid position 242 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at