Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_139343.3(BIN1):c.*82C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000158 in 152128 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Genome browser will be placed here
Verdict is Likely_benign. Variant got -4 ACMG points.
GnomAD3 genomes AF: 0.000158AC: 24AN: 152128Hom.: 0Cov.: 33 GnomAD4 exome AF: 0.000266AC: 328AN: 1232714Hom.: 2 AF XY: 0.000276AC XY: 172AN XY: 623622
Submissions by phenotype
Myopathy, centronuclear, 2
|Uncertain significance, criteria provided, single submitter
|Illumina Laboratory Services, Illumina
|Jan 13, 2018
|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. -
Find out detailed SpliceAI scores and Pangolin per-transcript scores at