rs3763558

Positions:

• chr8-96784503-C-A

Variant summary

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

The NM_016134.4(CPQ):​c.-34-361C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,798 control chromosomes in the GnomAD database, including 2,446 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 0.16 (2446 hom., cov: 31)
• Consequence: CPQ NM_016134.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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]

CPQ (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPQ	NM_016134.4	c.-34-361C>A		intron_variant		ENST00000220763.10	NP_057218.1
LOC124901985	XR_007061019.1	n.354+7039G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPQ	ENST00000220763.10	c.-34-361C>A		intron_variant		1	NM_016134.4	ENSP00000220763.5

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24669 AN: 151680 Hom.: 2442 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.148

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.163 AC: 24697 AN: 151798 Hom.: 2446 Cov.: 31 AF XY: 0.161 AC XY: 11973 AN XY: 74162

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0606

Gnomad4 SAS AF: 0.0915

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.155

Alfa AF: 0.119 Hom.: 1545

Bravo AF: 0.160

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.61

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: rs3763558; hg19: chr8-97796731;