rs17737465

Positions:

• chr8-97142213-A-G

Variant summary

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

The NM_016134.4(CPQ):​c.1256-807A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,250 control chromosomes in the GnomAD database, including 6,004 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 0.25 (6004 hom., cov: 33)
• Consequence: CPQ NM_016134.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

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]

LOC101927066 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPQ	NM_016134.4	c.1256-807A>G		intron_variant		ENST00000220763.10	NP_057218.1
LOC101927066	NR_125390.1	n.472-188603T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPQ	ENST00000220763.10	c.1256-807A>G		intron_variant		1	NM_016134.4	ENSP00000220763	P1
CPQ	ENST00000522617.3	c.229-807A>G		intron_variant		3		ENSP00000429134

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37803 AN: 152132 Hom.: 6001 Cov.: 33

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0167

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.248 AC: 37800 AN: 152250 Hom.: 6004 Cov.: 33 AF XY: 0.247 AC XY: 18393 AN XY: 74446

Gnomad4 AFR AF: 0.0777

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.259

Alfa AF: 0.306 Hom.: 4665

Bravo AF: 0.237

Asia WGS AF: 0.0840 AC: 291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.80
DANN	Benign	0.75

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: rs17737465; hg19: chr8-98154441;