16-53908893-T-C

Variant names:

• chr16-53908893-T-C
• rs12935710
• NM_001080432.3:c.1239+19942T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080432.3(FTO):​c.1239+19942T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,156 control chromosomes in the GnomAD database, including 41,234 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 0.73 (41234 hom., cov: 32)
• Consequence: FTO NM_001080432.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 11 publications found

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]

FTO Gene-Disease associations (from GenCC):

• lethal polymalformative syndrome, Boissel type

  Inheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FTO	NM_001080432.3	c.1239+19942T>C		intron_variant	Intron 7 of 8	ENST00000471389.6	NP_001073901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FTO	ENST00000471389.6	c.1239+19942T>C		intron_variant	Intron 7 of 8	1	NM_001080432.3	ENSP00000418823.1

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110555 AN: 152036 Hom.: 41228 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.727 AC: 110597 AN: 152156 Hom.: 41234 Cov.: 32 AF XY: 0.732 AC XY: 54440 AN XY: 74380

African (AFR) AF: 0.548 AC: 22718 AN: 41478

American (AMR) AF: 0.789 AC: 12066 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2787 AN: 3472

East Asian (EAS) AF: 0.977 AC: 5059 AN: 5176

South Asian (SAS) AF: 0.805 AC: 3876 AN: 4816

European-Finnish (FIN) AF: 0.832 AC: 8815 AN: 10592

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52825 AN: 68006

Other (OTH) AF: 0.733 AC: 1550 AN: 2114

Alfa AF: 0.759 Hom.: 67070

Bravo AF: 0.717

Asia WGS AF: 0.853 AC: 2968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	14
DANN	Benign	0.69
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12935710; hg19: chr16-53942805;