chr1-240258002-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020066.5(FMN2):c.4123C>A(p.Leu1375Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000341 in 1,612,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152122Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000201 AC: 50AN: 249218Hom.: 0 AF XY: 0.000238 AC XY: 32AN XY: 134702
GnomAD4 exome AF: 0.000347 AC: 507AN: 1459940Hom.: 0 Cov.: 30 AF XY: 0.000335 AC XY: 243AN XY: 726206
GnomAD4 genome AF: 0.000276 AC: 42AN: 152122Hom.: 0 Cov.: 33 AF XY: 0.000310 AC XY: 23AN XY: 74284
ClinVar
Submissions by phenotype
Intellectual disability, autosomal recessive 47 Uncertain:2
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
The variant c.4135C>A (p.Leu1379Ile) in the FMN2 gene is reported as of uncertain significance for autosomal recessive mental retardation 47 in ClinVar (Variation ID: 376966). The variant is reported with an estimated allele frequency of 0.0002 in gnomAD exomes and 0.0000646 in gnomAD genomes, with no homozygous individuals reported. The nucleotide position is moderately conserved across 35 mammalian species (GERP RS: 5.42). In silico analysis mostly indicates that the variant might be damaging. -
not specified Uncertain:1
- -
not provided Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at