chr8-17950651-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006197.4(PCM1):c.998G>A(p.Ser333Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000056 in 1,605,740 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
PCM1
NM_006197.4 missense
NM_006197.4 missense
Scores
4
3
9
Clinical Significance
Conservation
PhyloP100: 9.44
Genes affected
PCM1 (HGNC:8727): (pericentriolar material 1) The protein encoded by this gene is a component of centriolar satellites, which are electron dense granules scattered around centrosomes. Inhibition studies show that this protein is essential for the correct localization of several centrosomal proteins, and for anchoring microtubules to the centrosome. Chromosomal aberrations involving this gene are associated with papillary thyroid carcinomas and a variety of hematological malignancies, including atypical chronic myeloid leukemia and T-cell lymphoma. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.31810492).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCM1 | NM_006197.4 | c.998G>A | p.Ser333Asn | missense_variant | 8/39 | ENST00000325083.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCM1 | ENST00000325083.13 | c.998G>A | p.Ser333Asn | missense_variant | 8/39 | 1 | NM_006197.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152210Hom.: 0 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000168 AC: 4AN: 237808Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 128568
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GnomAD4 exome AF: 0.00000206 AC: 3AN: 1453530Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 722404
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74350
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.998G>A (p.S333N) alteration is located in exon 8 (coding exon 6) of the PCM1 gene. This alteration results from a G to A substitution at nucleotide position 998, causing the serine (S) at amino acid position 333 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N;N;N;N;N
REVEL
Benign
Sift
Uncertain
D;.;D;D;D;D;D
Sift4G
Benign
T;T;T;D;D;T;T
Polyphen
0.99
.;.;D;.;.;.;.
Vest4
MutPred
Loss of phosphorylation at S333 (P = 0.0485);Loss of phosphorylation at S333 (P = 0.0485);.;.;Loss of phosphorylation at S333 (P = 0.0485);Loss of phosphorylation at S333 (P = 0.0485);Loss of phosphorylation at S333 (P = 0.0485);
MVP
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at