14-103928607-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153046.3(TDRD9):c.98C>T(p.Pro33Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000338 in 1,331,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P33S) has been classified as Uncertain significance.
Frequency
Consequence
NM_153046.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000397 AC: 6AN: 151038Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000330 AC: 39AN: 1180782Hom.: 0 Cov.: 33 AF XY: 0.0000349 AC XY: 20AN XY: 572964
GnomAD4 genome AF: 0.0000397 AC: 6AN: 151146Hom.: 0 Cov.: 31 AF XY: 0.0000406 AC XY: 3AN XY: 73856
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.98C>T (p.P33L) alteration is located in exon 1 (coding exon 1) of the TDRD9 gene. This alteration results from a C to T substitution at nucleotide position 98, causing the proline (P) at amino acid position 33 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at