rs113638548
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001195248.2(APTX):c.*187G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00175 in 743,666 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001195248.2 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00535 AC: 814AN: 152134Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00112 AC: 152AN: 135794Hom.: 1 AF XY: 0.000978 AC XY: 72AN XY: 73654
GnomAD4 exome AF: 0.000807 AC: 477AN: 591414Hom.: 1 Cov.: 7 AF XY: 0.000684 AC XY: 217AN XY: 317314
GnomAD4 genome AF: 0.00542 AC: 825AN: 152252Hom.: 9 Cov.: 32 AF XY: 0.00527 AC XY: 392AN XY: 74434
ClinVar
Submissions by phenotype
Coenzyme Q10 deficiency, Oculomotor Apraxia Type Uncertain:1
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Ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia Benign: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 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. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at