rs9922047
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080432.3(FTO):c.46-37772C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,822 control chromosomes in the GnomAD database, including 26,043 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 0.58 ( 26043 hom., cov: 31)
Consequence
FTO
NM_001080432.3 intron
NM_001080432.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.701
Publications
30 publications found
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]
FTO Gene-Disease associations (from GenCC):
- lethal polymalformative syndrome, Boissel typeInheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
Genome browser will be placed here
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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.576 AC: 87452AN: 151704Hom.: 26005 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
87452
AN:
151704
Hom.:
Cov.:
31
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: 0.577 AC: 87537AN: 151822Hom.: 26043 Cov.: 31 AF XY: 0.574 AC XY: 42586AN XY: 74200 show subpopulations
GnomAD4 genome
AF:
AC:
87537
AN:
151822
Hom.:
Cov.:
31
AF XY:
AC XY:
42586
AN XY:
74200
show subpopulations
African (AFR)
AF:
AC:
30134
AN:
41406
American (AMR)
AF:
AC:
7326
AN:
15220
Ashkenazi Jewish (ASJ)
AF:
AC:
2108
AN:
3466
East Asian (EAS)
AF:
AC:
3326
AN:
5146
South Asian (SAS)
AF:
AC:
2376
AN:
4828
European-Finnish (FIN)
AF:
AC:
5394
AN:
10556
Middle Eastern (MID)
AF:
AC:
135
AN:
292
European-Non Finnish (NFE)
AF:
AC:
35087
AN:
67890
Other (OTH)
AF:
AC:
1192
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1815
3629
5444
7258
9073
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2077
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.