chr1-171282268-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001282693.2(FMO1):c.1118A>G(p.Lys373Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00258 in 1,613,910 control chromosomes in the GnomAD database, including 82 homozygotes. 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001282693.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMO1 | NM_001282693.2 | c.1118A>G | p.Lys373Arg | missense_variant | 7/9 | ENST00000617670.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMO1 | ENST00000617670.6 | c.1118A>G | p.Lys373Arg | missense_variant | 7/9 | 1 | NM_001282693.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0135 AC: 2049AN: 152132Hom.: 41 Cov.: 32
GnomAD3 exomes AF: 0.00376 AC: 937AN: 249378Hom.: 18 AF XY: 0.00270 AC XY: 365AN XY: 134982
GnomAD4 exome AF: 0.00145 AC: 2117AN: 1461660Hom.: 41 Cov.: 31 AF XY: 0.00123 AC XY: 894AN XY: 727132
GnomAD4 genome ? AF: 0.0135 AC: 2049AN: 152250Hom.: 41 Cov.: 32 AF XY: 0.0131 AC XY: 979AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at