rs1077128

Positions:

• chr16-53757741-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080432.3(FTO):​c.46-52399C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,926 control chromosomes in the GnomAD database, including 8,256 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 0.29 (8256 hom., cov: 32)
• Consequence: FTO NM_001080432.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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]

LOC124903691 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FTO	NM_001080432.3	c.46-52399C>A		intron_variant		ENST00000471389.6
LOC124903691	XR_007065070.1	n.219+10768G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FTO	ENST00000471389.6	c.46-52399C>A		intron_variant		1	NM_001080432.3	P1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43828 AN: 151810 Hom.: 8226 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.273

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.289 AC: 43907 AN: 151926 Hom.: 8256 Cov.: 32 AF XY: 0.283 AC XY: 20978 AN XY: 74254

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.277

Alfa AF: 0.232 Hom.: 1007

Bravo AF: 0.300

Asia WGS AF: 0.279 AC: 970 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.30
DANN	Benign	0.40

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

Other links and lift over

dbSNP: rs1077128; hg19: chr16-53791653;