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GeneBe

rs3751812

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001080432.3(FTO):c.46-25592G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151890 control chromosomes in the gnomAD Genomes database, including 8221 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 ( 8221 hom., cov: 31)

Consequence

FTO
NM_001080432.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.592

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BA1
?
GnomAd 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 UniProt
FTONM_001080432.3 linkuse as main transcriptc.46-25592G>T intron_variant ENST00000471389.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FTOENST00000471389.6 linkuse as main transcriptc.46-25592G>T intron_variant 1 NM_001080432.3 P1Q9C0B1-1

Frequencies

GnomAD3 genomes
AF:
0.298
AC:
45326
AN:
151890
Hom.:
8221
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0996
Gnomad AMI
AF:
0.462
Gnomad AMR
AF:
0.274
Gnomad ASJ
AF:
0.501
Gnomad EAS
AF:
0.152
Gnomad SAS
AF:
0.313
Gnomad FIN
AF:
0.399
Gnomad MID
AF:
0.364
Gnomad NFE
AF:
0.406
Gnomad OTH
AF:
0.321
Alfa
AF:
0.384
Hom.:
16948
Bravo
AF:
0.276
Asia WGS
AF:
0.266
AC:
927
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.43
Cadd
Benign
15
Dann
Benign
0.68

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: rs3751812; hg19: chr16-53818460; API