rs2853259

Variant names:

• chr8-96940737-T-C
• rs2853259
• NM_016134.4:c.850-25198T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016134.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPQ	NM_016134.4	MANE Select	c.850-25198T>C		intron	N/A	NP_057218.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPQ	ENST00000220763.10	TSL:1 MANE Select	c.850-25198T>C		intron	N/A	ENSP00000220763.5
	CPQ	ENST00000960277.1		c.850-21197T>C		intron	N/A	ENSP00000630336.1
	CPQ	ENST00000863818.1		c.850-21197T>C		intron	N/A	ENSP00000533877.1

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

African (AFR) AF: 0.383 AC: 15896 AN: 41484

American (AMR) AF: 0.382 AC: 5832 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1632 AN: 5176

South Asian (SAS) AF: 0.424 AC: 2044 AN: 4824

European-Finnish (FIN) AF: 0.369 AC: 3909 AN: 10584

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23651 AN: 67986

Other (OTH) AF: 0.366 AC: 773 AN: 2114

Alfa AF: 0.354 Hom.: 40414

Bravo AF: 0.368

Asia WGS AF: 0.392 AC: 1364 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.88
DANN	Benign	0.87
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2853259; hg19: chr8-97952965;