17-80107908-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000152.5(GAA):c.955+12G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 1,594,892 control chromosomes in the GnomAD database, including 403,769 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000152.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.655 AC: 99600AN: 151956Hom.: 33481 Cov.: 33
GnomAD3 exomes AF: 0.695 AC: 150388AN: 216458Hom.: 52770 AF XY: 0.706 AC XY: 83917AN XY: 118798
GnomAD4 exome AF: 0.714 AC: 1030860AN: 1442818Hom.: 370275 Cov.: 40 AF XY: 0.716 AC XY: 512901AN XY: 716836
GnomAD4 genome AF: 0.655 AC: 99644AN: 152074Hom.: 33494 Cov.: 33 AF XY: 0.653 AC XY: 48558AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:5
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not provided Uncertain:1Benign:3
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multiple AR variants in same gene - keep for nowAllele frequency is common in at least one population database (frequency: 82.703% in ExAC) based on the frequency threshold of 2.76% for this gene.Variant was observed in a homozygous state in population databases more than expected for disease.5 reputable source/s reports the variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.A synonymous variant not located in a splice region. -
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Glycogen storage disease, type II Benign:4
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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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at