rs748960946
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005391.5(PDK3):c.320+6T>C variant causes a splice region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000035 in 1,057,127 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_005391.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDK3 | ENST00000379162.9 | c.320+6T>C | splice_region_variant, intron_variant | Intron 3 of 10 | 1 | NM_005391.5 | ENSP00000368460.4 | |||
PDK3 | ENST00000568479.2 | c.320+6T>C | splice_region_variant, intron_variant | Intron 3 of 11 | 6 | ENSP00000498864.1 | ||||
PDK3 | ENST00000493226.2 | n.538T>C | non_coding_transcript_exon_variant | Exon 3 of 3 | 5 | |||||
PDK3 | ENST00000648777.1 | n.320+6T>C | splice_region_variant, intron_variant | Intron 3 of 11 | ENSP00000497727.1 |
Frequencies
GnomAD3 genomes AF: 0.00000907 AC: 1AN: 110195Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32471
GnomAD3 exomes AF: 0.0000212 AC: 3AN: 141405Hom.: 0 AF XY: 0.0000221 AC XY: 1AN XY: 45249
GnomAD4 exome AF: 0.0000380 AC: 36AN: 946932Hom.: 0 Cov.: 17 AF XY: 0.0000538 AC XY: 14AN XY: 260346
GnomAD4 genome AF: 0.00000907 AC: 1AN: 110195Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32471
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease X-linked dominant 6 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 26, 2024 | This sequence change falls in intron 3 of the PDK3 gene. It does not directly change the encoded amino acid sequence of the PDK3 protein. It affects a nucleotide within the consensus splice site. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with PDK3-related conditions. ClinVar contains an entry for this variant (Variation ID: 425484). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at