rs8050136
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080432.3(FTO):c.46-27777C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,066 control chromosomes in the GnomAD database, including 12,270 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 0.40 ( 12270 hom., cov: 32)
Consequence
FTO
NM_001080432.3 intron
NM_001080432.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.716
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.396 AC: 60202AN: 151948Hom.: 12261 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
60202
AN:
151948
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.396 AC: 60234AN: 152066Hom.: 12270 Cov.: 32 AF XY: 0.392 AC XY: 29148AN XY: 74314 show subpopulations
GnomAD4 genome
AF:
AC:
60234
AN:
152066
Hom.:
Cov.:
32
AF XY:
AC XY:
29148
AN XY:
74314
Gnomad4 AFR
AF:
AC:
0.437422
AN:
0.437422
Gnomad4 AMR
AF:
AC:
0.310325
AN:
0.310325
Gnomad4 ASJ
AF:
AC:
0.504608
AN:
0.504608
Gnomad4 EAS
AF:
AC:
0.151838
AN:
0.151838
Gnomad4 SAS
AF:
AC:
0.314238
AN:
0.314238
Gnomad4 FIN
AF:
AC:
0.399319
AN:
0.399319
Gnomad4 NFE
AF:
AC:
0.407838
AN:
0.407838
Gnomad4 OTH
AF:
AC:
0.390995
AN:
0.390995
Heterozygous variant carriers
0
1864
3729
5593
7458
9322
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
568
1136
1704
2272
2840
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1002
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at