chr8-96835102-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016134.4(CPQ):c.563C>T(p.Thr188Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000575 in 1,601,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016134.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPQ | NM_016134.4 | c.563C>T | p.Thr188Met | missense_variant | 3/8 | ENST00000220763.10 | NP_057218.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPQ | ENST00000220763.10 | c.563C>T | p.Thr188Met | missense_variant | 3/8 | 1 | NM_016134.4 | ENSP00000220763 | P1 | |
CPQ | ENST00000517742.1 | downstream_gene_variant | 5 | ENSP00000429146 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000377 AC: 9AN: 238714Hom.: 0 AF XY: 0.0000309 AC XY: 4AN XY: 129508
GnomAD4 exome AF: 0.0000600 AC: 87AN: 1448914Hom.: 0 Cov.: 29 AF XY: 0.0000527 AC XY: 38AN XY: 720710
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 15, 2024 | The c.563C>T (p.T188M) alteration is located in exon 3 (coding exon 2) of the CPQ gene. This alteration results from a C to T substitution at nucleotide position 563, causing the threonine (T) at amino acid position 188 to be replaced by a methionine (M). 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