16-53704180-GC-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001080432.3(FTO):c.-4del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,551,550 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00052 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000063 ( 0 hom. )
Consequence
FTO
NM_001080432.3 5_prime_UTR
NM_001080432.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.89
Genes affected
FTO (HGNC:24678): (FTO alpha-ketoglutarate dependent dioxygenase) This gene is a nuclear protein of the AlkB related non-haem iron and 2-oxoglutarate-dependent oxygenase superfamily but the exact physiological function of this gene is not known. Other non-heme iron enzymes function to reverse alkylated DNA and RNA damage by oxidative demethylation. Studies in mice and humans indicate a role in nervous and cardiovascular systems and a strong association with body mass index, obesity risk, and type 2 diabetes. [provided by RefSeq, Jul 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FTO | NM_001080432.3 | c.-4del | 5_prime_UTR_variant | 1/9 | ENST00000471389.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTO | ENST00000471389.6 | c.-4del | 5_prime_UTR_variant | 1/9 | 1 | NM_001080432.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000519 AC: 79AN: 152216Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000967 AC: 15AN: 155114Hom.: 0 AF XY: 0.0000612 AC XY: 5AN XY: 81748
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GnomAD4 exome AF: 0.0000629 AC: 88AN: 1399216Hom.: 0 Cov.: 30 AF XY: 0.0000420 AC XY: 29AN XY: 690130
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GnomAD4 genome AF: 0.000519 AC: 79AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74494
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lethal polymalformative syndrome, Boissel type Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at