rs2455044

Positions:

• chr8-96686014-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

ACMG classification

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: 106286 AN: 151256 Hom.: 37748 Cov.: 32

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

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

Other links and lift over

dbSNP: rs2455044; hg19: chr8-97698242;