rs782738200
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002024.6(FMR1):c.1580G>A(p.Arg527His) variant causes a missense change. The variant allele was found at a frequency of 0.0000174 in 1,204,066 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/16 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. R527S) has been classified as Uncertain significance.
Frequency
Consequence
NM_002024.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMR1 | NM_002024.6 | c.1580G>A | p.Arg527His | missense_variant | 15/17 | ENST00000370475.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMR1 | ENST00000370475.9 | c.1580G>A | p.Arg527His | missense_variant | 15/17 | 1 | NM_002024.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000909 AC: 1AN: 109963Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32213
GnomAD3 exomes AF: 0.0000288 AC: 5AN: 173482Hom.: 0 AF XY: 0.0000170 AC XY: 1AN XY: 58990
GnomAD4 exome AF: 0.0000183 AC: 20AN: 1094103Hom.: 0 Cov.: 33 AF XY: 0.0000139 AC XY: 5AN XY: 359905
GnomAD4 genome ? AF: 0.00000909 AC: 1AN: 109963Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32213
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2016 | Lines of evidence used in support of classification: UNCERTAIN: Alteration(s) of Uncertain Clinical Significance Detected - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at