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GeneBe

rs9939609

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080432.3(FTO):c.46-23525T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,992 control chromosomes in the GnomAD database, including 13,093 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 0.41 ( 13093 hom., cov: 32)

Consequence

FTO
NM_001080432.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.16
Variant links:
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=-0.47).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FTONM_001080432.3 linkuse as main transcriptc.46-23525T>A intron_variant ENST00000471389.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FTOENST00000471389.6 linkuse as main transcriptc.46-23525T>A intron_variant 1 NM_001080432.3 P1Q9C0B1-1

Frequencies

GnomAD3 genomes
AF:
0.408
AC:
62000
AN:
151874
Hom.:
13081
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.479
Gnomad AMI
AF:
0.464
Gnomad AMR
AF:
0.315
Gnomad ASJ
AF:
0.506
Gnomad EAS
AF:
0.155
Gnomad SAS
AF:
0.316
Gnomad FIN
AF:
0.399
Gnomad MID
AF:
0.396
Gnomad NFE
AF:
0.408
Gnomad OTH
AF:
0.400
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.408
AC:
62037
AN:
151992
Hom.:
13093
Cov.:
32
AF XY:
0.404
AC XY:
29989
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.479
Gnomad4 AMR
AF:
0.315
Gnomad4 ASJ
AF:
0.506
Gnomad4 EAS
AF:
0.155
Gnomad4 SAS
AF:
0.315
Gnomad4 FIN
AF:
0.399
Gnomad4 NFE
AF:
0.408
Gnomad4 OTH
AF:
0.401
Alfa
AF:
0.399
Hom.:
6955
Bravo
AF:
0.401
Asia WGS
AF:
0.294
AC:
1023
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
Cadd
Benign
7.0
Dann
Benign
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9939609; hg19: chr16-53820527; API