rs2853259

chr8-96940737-T-C

Variant summary

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

The NM_016134.4(CPQ):c.850-25198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,116 control chromosomes in the GnomAD database, including 10,102 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 0.36 (10102 hom., cov: 32)
• Consequence: CPQ NM_016134.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343

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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPQ	NM_016134.4	c.850-25198T>C		intron_variant		ENST00000220763.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPQ	ENST00000220763.10	c.850-25198T>C		intron_variant		1	NM_016134.4	P1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55263 AN: 151998 Hom.: 10091 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.364 AC: 55307 AN: 152116 Hom.: 10102 Cov.: 32 AF XY: 0.365 AC XY: 27147 AN XY: 74356

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.366

Alfa AF: 0.352 Hom.: 19435

Bravo AF: 0.368

Asia WGS AF: 0.392 AC: 1364 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	0.88
Dann	Benign	0.87

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: rs2853259; hg19: chr8-97952965;