rs4501570
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000370.3(TTPA):c.663+11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 1,586,250 control chromosomes in the GnomAD database, including 203,965 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000370.3 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: 0.592 AC: 89798AN: 151744Hom.: 28433 Cov.: 31
GnomAD3 exomes AF: 0.557 AC: 136191AN: 244296Hom.: 39827 AF XY: 0.544 AC XY: 71701AN XY: 131906
GnomAD4 exome AF: 0.486 AC: 697144AN: 1434388Hom.: 175485 Cov.: 27 AF XY: 0.487 AC XY: 348033AN XY: 714858
GnomAD4 genome AF: 0.592 AC: 89901AN: 151862Hom.: 28480 Cov.: 31 AF XY: 0.597 AC XY: 44312AN XY: 74186
ClinVar
Submissions by phenotype
Familial isolated deficiency of vitamin E 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. -
not provided Benign:3
Variant summary: The TTPA c.663+11T>C variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools via Alamut suggest no significant impact on a normal splicing pattern, however the functional studies confirming these predictions are yet to be conducted. This variant is present in EXAC at a frequency of 0.59 (63955/107728control chrs). The variant of interest is cites as Benign by reputable databases/clinical diagnostic laboratories. Taken together, based on the frequency in the general population, the variant was classified as Benign. -
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at