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GeneBe

rs1121980

Variant summary

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

The NM_001080432.3(FTO):c.46-34805G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,826 control chromosomes in the GnomAD database, including 14,452 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 0.43 ( 14452 hom., cov: 31)

Consequence

FTO
NM_001080432.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.31
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=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FTONM_001080432.3 linkuse as main transcriptc.46-34805G>A intron_variant ENST00000471389.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FTOENST00000471389.6 linkuse as main transcriptc.46-34805G>A intron_variant 1 NM_001080432.3 P1Q9C0B1-1

Frequencies

GnomAD3 genomes
AF:
0.432
AC:
65558
AN:
151710
Hom.:
14437
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.473
Gnomad AMI
AF:
0.485
Gnomad AMR
AF:
0.355
Gnomad ASJ
AF:
0.553
Gnomad EAS
AF:
0.197
Gnomad SAS
AF:
0.413
Gnomad FIN
AF:
0.432
Gnomad MID
AF:
0.418
Gnomad NFE
AF:
0.437
Gnomad OTH
AF:
0.429
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.432
AC:
65609
AN:
151826
Hom.:
14452
Cov.:
31
AF XY:
0.429
AC XY:
31836
AN XY:
74152
show subpopulations
Gnomad4 AFR
AF:
0.473
Gnomad4 AMR
AF:
0.356
Gnomad4 ASJ
AF:
0.553
Gnomad4 EAS
AF:
0.197
Gnomad4 SAS
AF:
0.413
Gnomad4 FIN
AF:
0.432
Gnomad4 NFE
AF:
0.437
Gnomad4 OTH
AF:
0.430
Alfa
AF:
0.427
Hom.:
27393
Bravo
AF:
0.422
Asia WGS
AF:
0.342
AC:
1188
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
0.024
Dann
Benign
0.37

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: rs1121980; hg19: chr16-53809247; API