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GeneBe

rs2455044

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.335
Variant links:
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
CPQNM_016134.4 linkuse as main transcriptc.-35+40612G>A intron_variant ENST00000220763.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CPQENST00000220763.10 linkuse as main transcriptc.-35+40612G>A intron_variant 1 NM_016134.4 P1
CPQENST00000517742.1 linkuse as main transcriptc.-35+26691G>A intron_variant 5
CPQENST00000519900.1 linkuse as main transcriptc.-35+5467G>A intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.703
AC:
106286
AN:
151256
Hom.:
37748
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.663
Gnomad AMI
AF:
0.659
Gnomad AMR
AF:
0.689
Gnomad ASJ
AF:
0.804
Gnomad EAS
AF:
0.402
Gnomad SAS
AF:
0.641
Gnomad FIN
AF:
0.723
Gnomad MID
AF:
0.811
Gnomad NFE
AF:
0.748
Gnomad OTH
AF:
0.726
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.703
AC:
106355
AN:
151374
Hom.:
37768
Cov.:
32
AF XY:
0.699
AC XY:
51676
AN XY:
73924
show subpopulations
Gnomad4 AFR
AF:
0.663
Gnomad4 AMR
AF:
0.689
Gnomad4 ASJ
AF:
0.804
Gnomad4 EAS
AF:
0.402
Gnomad4 SAS
AF:
0.642
Gnomad4 FIN
AF:
0.723
Gnomad4 NFE
AF:
0.748
Gnomad4 OTH
AF:
0.725
Alfa
AF:
0.735
Hom.:
5112
Bravo
AF:
0.699
Asia WGS
AF:
0.549
AC:
1897
AN:
3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
5.1
DANN
Benign
0.45

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2455044; hg19: chr8-97698242; API