Variant chr7-130322574-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_016352.4(CPA4):c.1164C>T(p.Thr388=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 1,614,002 control chromosomes in the GnomAD database, including 4,175 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 0.066 ( 360 hom., cov: 32)

Exomes 𝑓: 0.070 ( 3815 hom. )

Consequence

CPA4
NM_016352.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.147

Variant links:

Genes affected

CPA4 (HGNC:15740): (carboxypeptidase A4) This gene is a member of the carboxypeptidase A/B subfamily, and it is located in a cluster with three other family members on chromosome 7. Carboxypeptidases are zinc-containing exopeptidases that catalyze the release of carboxy-terminal amino acids, and are synthesized as zymogens that are activated by proteolytic cleavage. This gene could be involved in the histone hyperacetylation pathway. It is imprinted and may be a strong candidate gene for prostate cancer aggressiveness. [provided by RefSeq, Jul 2008]

CPA4 links:

LOC105375503 (HGNC:):

LOC105375503 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP7

Synonymous conserved (PhyloP=0.147 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPA4	NM_016352.4 linkuse as main transcript	c.1164C>T	p.Thr388=	synonymous_variant	11/11	ENST00000222482.10	NP_057436.2
LOC105375503	XR_001745362.2 linkuse as main transcript	n.104-1809G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPA4	ENST00000222482.10 linkuse as main transcript	c.1164C>T	p.Thr388=	synonymous_variant	11/11	1	NM_016352.4	ENSP00000222482	P1	Q9UI42-1
CPA4	ENST00000445470.6 linkuse as main transcript	c.1065C>T	p.Thr355=	synonymous_variant	10/10	2		ENSP00000412947		Q9UI42-2
CPA4	ENST00000493259.5 linkuse as main transcript	c.852C>T	p.Thr284=	synonymous_variant	9/9	2		ENSP00000419660

Frequencies

GnomAD3 genomes

AF:

0.0657

AC:

10003

AN:

152152

Hom.:

358

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0656

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0483

Gnomad ASJ

AF:

0.0703

Gnomad EAS

AF:

0.0135

Gnomad SAS

AF:

0.0286

Gnomad FIN

AF:

0.0515

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0785

Gnomad OTH

AF:

0.0737

GnomAD3 exomes

AF:

0.0571

AC:

14359

AN:

251342

Hom.:

460

AF XY:

0.0580

AC XY:

7872

AN XY:

135828

show subpopulations

Gnomad AFR exome

AF:

0.0613

Gnomad AMR exome

AF:

0.0337

Gnomad ASJ exome

AF:

0.0712

Gnomad EAS exome

AF:

0.0156

Gnomad SAS exome

AF:

0.0303

Gnomad FIN exome

AF:

0.0548

Gnomad NFE exome

AF:

0.0765

Gnomad OTH exome

AF:

0.0629

GnomAD4 exome

AF:

0.0702

AC:

102601

AN:

1461732

Hom.:

3815

Cov.:

AF XY:

0.0687

AC XY:

49957

AN XY:

727200

show subpopulations

Gnomad4 AFR exome

AF:

0.0655

Gnomad4 AMR exome

AF:

0.0372

Gnomad4 ASJ exome

AF:

0.0739

Gnomad4 EAS exome

AF:

0.0179

Gnomad4 SAS exome

AF:

0.0316

Gnomad4 FIN exome

AF:

0.0562

Gnomad4 NFE exome

AF:

0.0773

Gnomad4 OTH exome

AF:

0.0662

GnomAD4 genome

AF:

0.0658

AC:

10019

AN:

152270

Hom.:

360

Cov.:

AF XY:

0.0625

AC XY:

4654

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.0659

Gnomad4 AMR

AF:

0.0482

Gnomad4 ASJ

AF:

0.0703

Gnomad4 EAS

AF:

0.0135

Gnomad4 SAS

AF:

0.0286

Gnomad4 FIN

AF:

0.0515

Gnomad4 NFE

AF:

0.0785

Gnomad4 OTH

AF:

0.0729

Alfa

AF:

0.0733

Hom.:

712

Bravo

AF:

0.0653

Asia WGS

AF:

0.0200

AC:

AN:

3478

EpiCase

AF:

0.0775

EpiControl

AF:

0.0744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

3.3

DANN

Benign

0.80

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over