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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPD	NM_001304.5	c.994+8487A>C		intron_variant	Intron 2 of 20	ENST00000225719.9	NP_001295.2
CPD	NM_001199775.1	c.253+8487A>C		intron_variant	Intron 2 of 20		NP_001186704.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPD	ENST00000225719.9	c.994+8487A>C		intron_variant	Intron 2 of 20	1	NM_001304.5	ENSP00000225719.4
CPD	ENST00000543464.6	c.253+8487A>C		intron_variant	Intron 2 of 20	2		ENSP00000444443.2

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 v4.3

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Other links and lift over

dbSNP: rs3794794; hg19: chr17-28720741;