16-53704142-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001363894.1(FTO):c.-43G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000365 in 1,547,300 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001363894.1 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000374 AC: 57AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000666 AC: 104AN: 156090Hom.: 0 AF XY: 0.000633 AC XY: 52AN XY: 82172
GnomAD4 exome AF: 0.000364 AC: 508AN: 1395066Hom.: 0 Cov.: 29 AF XY: 0.000368 AC XY: 253AN XY: 688374
GnomAD4 genome AF: 0.000374 AC: 57AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74374
ClinVar
Submissions by phenotype
Lethal polymalformative syndrome, Boissel type Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at