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GeneBe

rs8050136

chr16-53782363-C-A

Variant summary

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

The NM_001080432.3(FTO):c.46-27777C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151948 control chromosomes in the gnomAD Genomes database, including 12261 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 0.40 ( 12261 hom., cov: 32)

Consequence

FTO
NM_001080432.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.716

Links

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
?
GnomAd highest subpopulation (AFR) 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.46-27777C>A intron_variant ENST00000471389.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FTOENST00000471389.6 linkuse as main transcriptc.46-27777C>A intron_variant 1 NM_001080432.3 P1Q9C0B1-1

Frequencies

GnomAD3 genomes
AF:
0.396
AC:
60202
AN:
151948
Hom.:
12261
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.438
Gnomad AMI
AF:
0.464
Gnomad AMR
AF:
0.311
Gnomad ASJ
AF:
0.505
Gnomad EAS
AF:
0.152
Gnomad SAS
AF:
0.315
Gnomad FIN
AF:
0.399
Gnomad MID
AF:
0.396
Gnomad NFE
AF:
0.408
Gnomad OTH
AF:
0.390
Alfa
AF:
0.397
Hom.:
28397
Bravo
AF:
0.387
Asia WGS
AF:
0.288
AC:
1002
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
4.1
Dann
Benign
0.62

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: rs8050136; hg19: chr16-53816275;