chr9-92332277-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001012267.3(CENPP):c.215C>T(p.Thr72Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.003 in 1,612,096 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001012267.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPP | NM_001012267.3 | c.215C>T | p.Thr72Met | missense_variant | 2/8 | ENST00000375587.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPP | ENST00000375587.8 | c.215C>T | p.Thr72Met | missense_variant | 2/8 | 1 | NM_001012267.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00237 AC: 361AN: 152056Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00216 AC: 539AN: 249942Hom.: 3 AF XY: 0.00216 AC XY: 292AN XY: 135144
GnomAD4 exome AF: 0.00307 AC: 4480AN: 1459922Hom.: 13 Cov.: 30 AF XY: 0.00291 AC XY: 2113AN XY: 726326
GnomAD4 genome ? AF: 0.00238 AC: 362AN: 152174Hom.: 1 Cov.: 33 AF XY: 0.00208 AC XY: 155AN XY: 74426
ClinVar
Submissions by phenotype
CENPP-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 28, 2020 | This variant is classified as likely 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