rs1532047

Variant names:

• chr7-130344948-G-A
• rs1532047
• NM_080385.5:c.-409G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-130344948-G-A
• chr7-130344948-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_080385.5(CPA5):​c.-409G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,002 control chromosomes in the GnomAD database, including 27,590 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 0.60 (27590 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CPA5 NM_080385.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91
• Publications: 9 publications found

Genes affected

CPA5 (HGNC:15722): (carboxypeptidase A5) Carboxypeptidases have functions ranging from digestion of food to selective biosynthesis of neuroendocrine peptides. Members of the A/B subfamily of carboxypeptidases, such as CPA5, contain an approximately 90-amino acid pro region that assists in the folding of the active carboxypeptidase domain. Cleavage of the pro region activates the enzyme (Wei et al., 2002 [PubMed 11836249]).[supplied by OMIM, Mar 2008]

LOC105375503 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080385.5. 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
	CPA5	NM_080385.5	MANE Select	c.-409G>A		5_prime_UTR	Exon 1 of 13	NP_525124.3
	CPA5	NM_001127441.2		c.-462G>A		5_prime_UTR	Exon 1 of 14	NP_001120913.1	Q8WXQ8-1
	CPA5	NM_001318223.2		c.-351G>A		5_prime_UTR	Exon 1 of 12	NP_001305152.1	Q8WXQ8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPA5	ENST00000474905.6	TSL:1 MANE Select	c.-409G>A		5_prime_UTR	Exon 1 of 13	ENSP00000417314.1	Q8WXQ8-1
	CPA5	ENST00000461828.5	TSL:1	c.-351G>A		5_prime_UTR	Exon 1 of 12	ENSP00000418183.1	Q8WXQ8-1
	CPA5	ENST00000485477.5	TSL:1	c.-1028G>A		5_prime_UTR	Exon 1 of 12	ENSP00000420237.1	Q8WXQ8-1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91226 AN: 151884 Hom.: 27573 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.602

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.601 AC: 91289 AN: 152002 Hom.: 27590 Cov.: 32 AF XY: 0.597 AC XY: 44355 AN XY: 74282

African (AFR) AF: 0.650 AC: 26968 AN: 41458

American (AMR) AF: 0.624 AC: 9539 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2158 AN: 3468

East Asian (EAS) AF: 0.537 AC: 2774 AN: 5166

South Asian (SAS) AF: 0.559 AC: 2688 AN: 4808

European-Finnish (FIN) AF: 0.551 AC: 5820 AN: 10564

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39432 AN: 67942

Other (OTH) AF: 0.604 AC: 1273 AN: 2108

Alfa AF: 0.570 Hom.: 13413

Bravo AF: 0.607

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	15
DANN	Benign	0.64
PhyloP100		1.9
PromoterAI		-0.025	Neutral
Mutation Taster		=292/8	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: rs1532047; hg19: chr7-129984788;