3-180912713-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_005087.4(FXR1):c.28G>T(p.Gly10Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000658 in 152,006 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. G10G) has been classified as Likely benign.
Frequency
Consequence
NM_005087.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FXR1 | NM_005087.4 | c.28G>T | p.Gly10Cys | missense_variant | 1/17 | ENST00000357559.9 | |
FXR1 | NM_001013438.3 | c.28G>T | p.Gly10Cys | missense_variant | 1/16 | ||
FXR1 | NM_001013439.3 | c.-572G>T | 5_prime_UTR_variant | 1/18 | |||
FXR1 | NM_001363882.1 | c.-572G>T | 5_prime_UTR_variant | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FXR1 | ENST00000357559.9 | c.28G>T | p.Gly10Cys | missense_variant | 1/17 | 1 | NM_005087.4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152006Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 34
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152006Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74230
ClinVar
Submissions by phenotype
Myopathy, congenital, with respiratory insufficiency and bone fractures Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | May 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at