chr16-67828803-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_025082.4(CENPT):āc.1321C>Gā(p.Pro441Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00051 in 1,596,282 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_025082.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPT | NM_025082.4 | c.1321C>G | p.Pro441Ala | missense_variant | 14/16 | ENST00000562787.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPT | ENST00000562787.6 | c.1321C>G | p.Pro441Ala | missense_variant | 14/16 | 2 | NM_025082.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000499 AC: 76AN: 152170Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00101 AC: 230AN: 227300Hom.: 1 AF XY: 0.000951 AC XY: 118AN XY: 124078
GnomAD4 exome AF: 0.000511 AC: 738AN: 1443994Hom.: 7 Cov.: 33 AF XY: 0.000519 AC XY: 373AN XY: 718478
GnomAD4 genome AF: 0.000499 AC: 76AN: 152288Hom.: 1 Cov.: 32 AF XY: 0.000551 AC XY: 41AN XY: 74460
ClinVar
Submissions by phenotype
CENPT-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 28, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at