rs6982224

Positions:

• chr8-96853262-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.641+18082G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,034 control chromosomes in the GnomAD database, including 20,433 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 0.51 (20433 hom., cov: 32)
• Consequence: CPQ NM_016134.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPQ	NM_016134.4	c.641+18082G>A		intron_variant		ENST00000220763.10	NP_057218.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPQ	ENST00000220763.10	c.641+18082G>A		intron_variant		1	NM_016134.4	ENSP00000220763	P1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77760 AN: 151916 Hom.: 20410 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.512 AC: 77837 AN: 152034 Hom.: 20433 Cov.: 32 AF XY: 0.508 AC XY: 37762 AN XY: 74312

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.497

Alfa AF: 0.502 Hom.: 3310

Bravo AF: 0.520

Asia WGS AF: 0.405 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.74

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: rs6982224; hg19: chr8-97865490;