rs769703635
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020066.5(FMN2):c.953C>T(p.Pro318Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,394,666 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_020066.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMN2 | NM_020066.5 | c.953C>T | p.Pro318Leu | missense_variant | 1/18 | ENST00000319653.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMN2 | ENST00000319653.14 | c.953C>T | p.Pro318Leu | missense_variant | 1/18 | 5 | NM_020066.5 | P1 | |
FMN2 | ENST00000447095.5 | c.-87+24989C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000128 AC: 2AN: 15612Hom.: 0 AF XY: 0.000246 AC XY: 2AN XY: 8136
GnomAD4 exome AF: 0.000127 AC: 158AN: 1242484Hom.: 0 Cov.: 87 AF XY: 0.000140 AC XY: 84AN XY: 601222
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 06, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at