NM_016352.4:c.1079-4231G>A

Variant names:

• chr7-130318258-G-A
• rs1488009
• NM_016352.4:c.1079-4231G>A

Variant summary

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

The NM_016352.4(CPA4):​c.1079-4231G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,064 control chromosomes in the GnomAD database, including 59,324 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 0.88 (59324 hom., cov: 30)
• Consequence: CPA4 NM_016352.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 2 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016352.4. 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
	CPA4	NM_016352.4	MANE Select	c.1079-4231G>A		intron	N/A	NP_057436.2
	CPA4	NM_001163446.2		c.980-4231G>A		intron	N/A	NP_001156918.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPA4	ENST00000222482.10	TSL:1 MANE Select	c.1079-4231G>A		intron	N/A	ENSP00000222482.4
	CPA4	ENST00000445470.6	TSL:2	c.980-4231G>A		intron	N/A	ENSP00000412947.2
	CPA4	ENST00000493259.5	TSL:2	c.767-4231G>A		intron	N/A	ENSP00000419660.1

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133923 AN: 151946 Hom.: 59286 Cov.: 30

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.881 AC: 134019 AN: 152064 Hom.: 59324 Cov.: 30 AF XY: 0.888 AC XY: 66031 AN XY: 74330

African (AFR) AF: 0.804 AC: 33313 AN: 41432

American (AMR) AF: 0.918 AC: 14025 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3144 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5089 AN: 5162

South Asian (SAS) AF: 0.967 AC: 4655 AN: 4816

European-Finnish (FIN) AF: 0.936 AC: 9904 AN: 10582

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60886 AN: 68008

Other (OTH) AF: 0.889 AC: 1879 AN: 2114

Alfa AF: 0.894 Hom.: 102562

Bravo AF: 0.877

Asia WGS AF: 0.968 AC: 3367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.61
PhyloP100		0.30
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: rs1488009; hg19: chr7-129958098;