rs9937053

Variant summary

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

The NM_001080432.3(FTO):​c.46-44545G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 150,544 control chromosomes in the GnomAD database, including 13,303 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 0.42 ( 13303 hom., cov: 28)

Consequence

FTO
NM_001080432.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0290
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=-0.97).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FTONM_001080432.3 linkuse as main transcriptc.46-44545G>A intron_variant ENST00000471389.6
LOC124903691XR_007065070.1 linkuse as main transcriptn.219+2914C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FTOENST00000471389.6 linkuse as main transcriptc.46-44545G>A intron_variant 1 NM_001080432.3 P1Q9C0B1-1

Frequencies

GnomAD3 genomes
AF:
0.416
AC:
62626
AN:
150442
Hom.:
13295
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.421
Gnomad AMI
AF:
0.490
Gnomad AMR
AF:
0.349
Gnomad ASJ
AF:
0.549
Gnomad EAS
AF:
0.196
Gnomad SAS
AF:
0.413
Gnomad FIN
AF:
0.423
Gnomad MID
AF:
0.410
Gnomad NFE
AF:
0.436
Gnomad OTH
AF:
0.416
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.416
AC:
62660
AN:
150544
Hom.:
13303
Cov.:
28
AF XY:
0.414
AC XY:
30351
AN XY:
73380
show subpopulations
Gnomad4 AFR
AF:
0.421
Gnomad4 AMR
AF:
0.349
Gnomad4 ASJ
AF:
0.549
Gnomad4 EAS
AF:
0.196
Gnomad4 SAS
AF:
0.413
Gnomad4 FIN
AF:
0.423
Gnomad4 NFE
AF:
0.436
Gnomad4 OTH
AF:
0.417
Alfa
AF:
0.400
Hom.:
5142
Bravo
AF:
0.405
Asia WGS
AF:
0.334
AC:
1162
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
2.8
DANN
Benign
0.71

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: rs9937053; hg19: chr16-53799507; API