X-147929961-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002024.6(FMR1):c.433G>T(p.Ala145Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00499 in 1,191,575 control chromosomes in the GnomAD database, including 192 homozygotes. There are 1,528 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A145V) has been classified as Uncertain significance.
Frequency
Consequence
NM_002024.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMR1 | NM_002024.6 | c.433G>T | p.Ala145Ser | missense_variant | 6/17 | ENST00000370475.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMR1 | ENST00000370475.9 | c.433G>T | p.Ala145Ser | missense_variant | 6/17 | 1 | NM_002024.6 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0254 AC: 2820AN: 110893Hom.: 103 Cov.: 22 AF XY: 0.0217 AC XY: 721AN XY: 33203
GnomAD3 exomes AF: 0.00772 AC: 1396AN: 180837Hom.: 48 AF XY: 0.00445 AC XY: 293AN XY: 65783
GnomAD4 exome AF: 0.00289 AC: 3122AN: 1080631Hom.: 89 Cov.: 28 AF XY: 0.00230 AC XY: 801AN XY: 348921
GnomAD4 genome AF: 0.0255 AC: 2826AN: 110944Hom.: 103 Cov.: 22 AF XY: 0.0219 AC XY: 727AN XY: 33264
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 26, 2018 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 24, 2014 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Fragile X syndrome Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Fragile X syndrome;C1839780:Fragile X-associated tremor/ataxia syndrome;C4552079:Premature ovarian failure 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 12, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at