rs3794794

Variant names:

• chr17-30393723-A-C
• rs3794794
• NM_001304.5:c.994+8487A>C

Your query was ambiguous. Multiple possible variants found:

• chr17-30393723-A-C
• chr17-30393723-A-G
• chr17-30393723-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001304.5(CPD):​c.994+8487A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,052 control chromosomes in the GnomAD database, including 15,754 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 0.44 (15754 hom., cov: 32)
• Consequence: CPD NM_001304.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473
• Publications: 17 publications found

Genes affected

CPD (HGNC:2301): (carboxypeptidase D) The metallocarboxypeptidase family of enzymes is divided into 2 subfamilies based on sequence similarities. The pancreatic carboxypeptidase-like and the regulatory B-type carboxypeptidase subfamilies. Carboxypeptidase D has been identified as a regulatory B-type carboxypeptidase. CPD is a homolog of duck gp180, a hepatitis B virus-binding protein. Transcript variants utilizing alternative polyadenylation signals exist for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPD	NM_001304.5	MANE Select	c.994+8487A>C		intron	N/A	NP_001295.2
	CPD	NM_001199775.1		c.253+8487A>C		intron	N/A	NP_001186704.1	O75976-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPD	ENST00000225719.9	TSL:1 MANE Select	c.994+8487A>C		intron	N/A	ENSP00000225719.4	O75976-1
	CPD	ENST00000892708.1		c.994+8487A>C		intron	N/A	ENSP00000562767.1
	CPD	ENST00000961764.1		c.994+8487A>C		intron	N/A	ENSP00000631823.1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67511 AN: 151934 Hom.: 15749 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.444 AC: 67533 AN: 152052 Hom.: 15754 Cov.: 32 AF XY: 0.449 AC XY: 33346 AN XY: 74294

African (AFR) AF: 0.354 AC: 14677 AN: 41448

American (AMR) AF: 0.493 AC: 7538 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1677 AN: 3468

East Asian (EAS) AF: 0.833 AC: 4321 AN: 5190

South Asian (SAS) AF: 0.517 AC: 2497 AN: 4828

European-Finnish (FIN) AF: 0.420 AC: 4436 AN: 10550

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30853 AN: 67972

Other (OTH) AF: 0.465 AC: 982 AN: 2110

Alfa AF: 0.458 Hom.: 51357

Bravo AF: 0.448

Asia WGS AF: 0.622 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.53
PhyloP100		0.47
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: rs3794794; hg19: chr17-28720741;