rs2234889
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001460.5(FMO2):c.1588del(p.Cys530AlafsTer23) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
FMO2
NM_001460.5 frameshift
NM_001460.5 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.47
Genes affected
FMO2 (HGNC:3770): (flavin containing dimethylaniline monoxygenase 2) This gene encodes a flavin-containing monooxygenase family member. It is an NADPH-dependent enzyme that catalyzes the N-oxidation of some primary alkylamines through an N-hydroxylamine intermediate. However, some human populations contain an allele (FMO2*2A) with a premature stop codon, resulting in a protein that is C-terminally-truncated, has no catalytic activity, and is likely degraded rapidly. This gene is found in a cluster with other related family members on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMO2 | NM_001460.5 | c.1588del | p.Cys530AlafsTer23 | frameshift_variant | 9/9 | ENST00000209929.10 | |
LOC124900413 | XR_007066731.1 | n.366-12181del | intron_variant, non_coding_transcript_variant | ||||
LOC105371611 | XR_922278.4 | n.514+38462del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMO2 | ENST00000209929.10 | c.1588del | p.Cys530AlafsTer23 | frameshift_variant | 9/9 | 1 | NM_001460.5 | P1 | |
ENST00000445290.1 | n.139-9604del | intron_variant, non_coding_transcript_variant | 2 | ||||||
ENST00000669750.1 | n.448+38447del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 genomes
?
Cov.:
30
GnomAD4 exome AF: 0.0000246 AC: 13AN: 527618Hom.: 0 Cov.: 7 AF XY: 0.0000218 AC XY: 6AN XY: 275314
GnomAD4 exome
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AC:
13
AN:
527618
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Cov.:
7
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6
AN XY:
275314
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GnomAD4 genome ? Cov.: 30
GnomAD4 genome
?
Cov.:
30
ClinVar
Not reported inComputational scores
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Name
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.