chrX-147981437-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_152578.3(FMR1NB):c.35A>G(p.Asn12Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,209,296 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 26 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_152578.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMR1NB | NM_152578.3 | c.35A>G | p.Asn12Ser | missense_variant | 1/6 | ENST00000370467.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMR1NB | ENST00000370467.8 | c.35A>G | p.Asn12Ser | missense_variant | 1/6 | 1 | NM_152578.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000180 AC: 2AN: 111234Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33434
GnomAD3 exomes AF: 0.0000874 AC: 16AN: 182998Hom.: 0 AF XY: 0.000148 AC XY: 10AN XY: 67464
GnomAD4 exome AF: 0.0000392 AC: 43AN: 1098062Hom.: 0 Cov.: 34 AF XY: 0.0000715 AC XY: 26AN XY: 363428
GnomAD4 genome ? AF: 0.0000180 AC: 2AN: 111234Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.35A>G (p.N12S) alteration is located in exon 1 (coding exon 1) of the FMR1NB gene. This alteration results from a A to G substitution at nucleotide position 35, causing the asparagine (N) at amino acid position 12 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | FMR1NB: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at