rs34452707
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_018319.4(TDP1):c.911G>A(p.Arg304Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00119 in 1,614,010 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_018319.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TDP1 | NM_018319.4 | c.911G>A | p.Arg304Gln | missense_variant | Exon 9 of 17 | ENST00000335725.9 | NP_060789.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00590 AC: 897AN: 152048Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00156 AC: 392AN: 251258Hom.: 4 AF XY: 0.00107 AC XY: 145AN XY: 135810
GnomAD4 exome AF: 0.000692 AC: 1011AN: 1461844Hom.: 13 Cov.: 33 AF XY: 0.000612 AC XY: 445AN XY: 727234
GnomAD4 genome AF: 0.00597 AC: 908AN: 152166Hom.: 6 Cov.: 32 AF XY: 0.00601 AC XY: 447AN XY: 74398
ClinVar
Submissions by phenotype
not provided Benign:4
- -
See Variant Classification Assertion Criteria. -
- -
- -
not specified Benign:2
- -
- -
Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at