rs17817497

Variant summary

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

The ENST00000471389.6(FTO):​c.46-28617T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,104 control chromosomes in the GnomAD database, including 8,243 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 0.30 ( 8243 hom., cov: 31)

Consequence

FTO
ENST00000471389.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.145
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FTONM_001080432.3 linkuse as main transcriptc.46-28617T>C intron_variant ENST00000471389.6 NP_001073901.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FTOENST00000471389.6 linkuse as main transcriptc.46-28617T>C intron_variant 1 NM_001080432.3 ENSP00000418823 P1Q9C0B1-1

Frequencies

GnomAD3 genomes
AF:
0.298
AC:
45264
AN:
151986
Hom.:
8246
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0962
Gnomad AMI
AF:
0.464
Gnomad AMR
AF:
0.273
Gnomad ASJ
AF:
0.499
Gnomad EAS
AF:
0.152
Gnomad SAS
AF:
0.316
Gnomad FIN
AF:
0.400
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.406
Gnomad OTH
AF:
0.322
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.297
AC:
45249
AN:
152104
Hom.:
8243
Cov.:
31
AF XY:
0.297
AC XY:
22118
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.0959
Gnomad4 AMR
AF:
0.273
Gnomad4 ASJ
AF:
0.499
Gnomad4 EAS
AF:
0.152
Gnomad4 SAS
AF:
0.316
Gnomad4 FIN
AF:
0.400
Gnomad4 NFE
AF:
0.406
Gnomad4 OTH
AF:
0.324
Alfa
AF:
0.381
Hom.:
2816
Bravo
AF:
0.275
Asia WGS
AF:
0.270
AC:
938
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
2.8
DANN
Benign
0.80

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: rs17817497; hg19: chr16-53815435; API