9-32973205-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001195248.2(APTX):c.*293C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 531,222 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001195248.2 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000821 AC: 125AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00186 AC: 244AN: 130852Hom.: 1 AF XY: 0.00218 AC XY: 155AN XY: 71248
GnomAD4 exome AF: 0.00181 AC: 685AN: 378906Hom.: 5 Cov.: 0 AF XY: 0.00214 AC XY: 450AN XY: 210450
GnomAD4 genome AF: 0.000821 AC: 125AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000846 AC XY: 63AN XY: 74478
ClinVar
Submissions by phenotype
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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at