rs11076022
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080432.3(FTO):c.*5151A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,096 control chromosomes in the GnomAD database, including 10,141 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.34 ( 10140 hom., cov: 32)
Exomes 𝑓: 0.31 ( 1 hom. )
Consequence
FTO
NM_001080432.3 3_prime_UTR
NM_001080432.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.15
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FTO | NM_001080432.3 | c.*5151A>G | 3_prime_UTR_variant | 9/9 | ENST00000471389.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FTO | ENST00000471389.6 | c.*5151A>G | 3_prime_UTR_variant | 9/9 | 1 | NM_001080432.3 | P1 | ||
FTO | ENST00000612285.2 | c.517+5177A>G | intron_variant | 5 | |||||
FTO | ENST00000637969.1 | c.1492+5177A>G | intron_variant | 5 | |||||
FTO | ENST00000637845.1 | c.1493-1315A>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.344 AC: 52235AN: 151962Hom.: 10139 Cov.: 32
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GnomAD4 exome AF: 0.313 AC: 5AN: 16Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 2AN XY: 8
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GnomAD4 genome ? AF: 0.344 AC: 52258AN: 152080Hom.: 10140 Cov.: 32 AF XY: 0.350 AC XY: 26019AN XY: 74346
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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