chrX-148024929-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_152578.3(FMR1NB):āc.697A>Gā(p.Arg233Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,097,609 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_152578.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMR1NB | NM_152578.3 | c.697A>G | p.Arg233Gly | missense_variant | 5/6 | ENST00000370467.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMR1NB | ENST00000370467.8 | c.697A>G | p.Arg233Gly | missense_variant | 5/6 | 1 | NM_152578.3 | P1 | |
FMR1NB | ENST00000489034.2 | c.187A>G | p.Arg63Gly | missense_variant, NMD_transcript_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.0000437 AC: 8AN: 182942Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67548
GnomAD4 exome AF: 0.0000446 AC: 49AN: 1097609Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 17AN XY: 363187
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.697A>G (p.R233G) alteration is located in exon 5 (coding exon 5) of the FMR1NB gene. This alteration results from a A to G substitution at nucleotide position 697, causing the arginine (R) at amino acid position 233 to be replaced by a glycine (G). 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