rs2455044
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016134.4(CPQ):c.-35+40612G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,374 control chromosomes in the GnomAD database, including 37,768 homozygotes. 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
Genomes: 𝑓 0.70 ( 37768 hom., cov: 32)
Consequence
CPQ
NM_016134.4 intron
NM_016134.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.335
Genes affected
CPQ (HGNC:16910): (carboxypeptidase Q) This gene encodes a metallopeptidase that belongs to the peptidase M28 family. The encoded protein may catalyze the cleavage of dipeptides with unsubstituted terminals into amino acids. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPQ | NM_016134.4 | c.-35+40612G>A | intron_variant | ENST00000220763.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPQ | ENST00000220763.10 | c.-35+40612G>A | intron_variant | 1 | NM_016134.4 | P1 | |||
CPQ | ENST00000517742.1 | c.-35+26691G>A | intron_variant | 5 | |||||
CPQ | ENST00000519900.1 | c.-35+5467G>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.703 AC: 106286AN: 151256Hom.: 37748 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.703 AC: 106355AN: 151374Hom.: 37768 Cov.: 32 AF XY: 0.699 AC XY: 51676AN XY: 73924
GnomAD4 genome
?
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106355
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32
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51676
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73924
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Asia WGS
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1897
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3458
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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