chr16-53875273-G-T

Position:

• chr16-53875273-G-T

Variant summary

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

The ENST00000471389.6(FTO):​c.975+1408G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,928 control chromosomes in the GnomAD database, including 20,425 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 0.51 (20425 hom., cov: 32)
• Consequence: FTO ENST00000471389.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FTO	NM_001080432.3	c.975+1408G>T		intron_variant		ENST00000471389.6	NP_001073901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FTO	ENST00000471389.6	c.975+1408G>T		intron_variant		1	NM_001080432.3	ENSP00000418823	P1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77679 AN: 151810 Hom.: 20398 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.512 AC: 77751 AN: 151928 Hom.: 20425 Cov.: 32 AF XY: 0.513 AC XY: 38119 AN XY: 74252

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.471

Alfa AF: 0.463 Hom.: 14810

Bravo AF: 0.522

Asia WGS AF: 0.613 AC: 2132 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.50

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: rs10521303; hg19: chr16-53909185;