16-67828838-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_025082.4(CENPT):c.1286C>T(p.Ser429Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000949 in 1,580,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_025082.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CENPT | NM_025082.4 | c.1286C>T | p.Ser429Phe | missense_variant | 14/16 | ENST00000562787.6 | NP_079358.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CENPT | ENST00000562787.6 | c.1286C>T | p.Ser429Phe | missense_variant | 14/16 | 2 | NM_025082.4 | ENSP00000457810.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000141 AC: 3AN: 212576Hom.: 0 AF XY: 0.00000859 AC XY: 1AN XY: 116416
GnomAD4 exome AF: 0.00000770 AC: 11AN: 1427758Hom.: 0 Cov.: 33 AF XY: 0.00000704 AC XY: 5AN XY: 709896
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152350Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 22, 2024 | The c.1286C>T (p.S429F) alteration is located in exon 14 (coding exon 11) of the CENPT gene. This alteration results from a C to T substitution at nucleotide position 1286, causing the serine (S) at amino acid position 429 to be replaced by a phenylalanine (F). 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