rs73215937

chr3-132356915-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001099.5(ACP3):c.*37T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 1,577,902 control chromosomes in the GnomAD database, including 21,844 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 0.12 (1403 hom., cov: 32)
  • Exomes 𝑓: 0.16 (20441 hom.)
• Consequence: ACP3 NM_001099.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

Genes affected

ACP3 (HGNC:125): (acid phosphatase 3) This gene encodes an enzyme that catalyzes the conversion of orthophosphoric monoester to alcohol and orthophosphate. It is synthesized under androgen regulation and is secreted by the epithelial cells of the prostate gland. An alternatively spliced transcript variant encoding a longer isoform has been found for this gene. This isoform contains a transmembrane domain and is localized in the plasma membrane-endosomal-lysosomal pathway. [provided by RefSeq, Sep 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACP3	NM_001099.5	c.*37T>C		3_prime_UTR_variant	10/10	ENST00000336375.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACP3	ENST00000336375.10	c.*37T>C		3_prime_UTR_variant	10/10	1	NM_001099.5
ACP3	ENST00000475741.5	c.*37T>C		3_prime_UTR_variant	9/9	1
ACP3	ENST00000351273.12	c.1138+60T>C		intron_variant		1		P1
ACP3	ENST00000507647.1	c.192+60T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18957 AN: 152054 Hom.: 1401 Cov.: 32

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0977

Gnomad EAS AF: 0.0424

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.147

GnomAD3 exomes AF: 0.131 AC: 30525 AN: 232388 Hom.: 2330 AF XY: 0.137 AC XY: 17220 AN XY: 126094

Gnomad AFR exome AF: 0.0541

Gnomad AMR exome AF: 0.0895

Gnomad ASJ exome AF: 0.0939

Gnomad EAS exome AF: 0.0369

Gnomad SAS exome AF: 0.167

Gnomad FIN exome AF: 0.111

Gnomad NFE exome AF: 0.167

Gnomad OTH exome AF: 0.133

GnomAD4 exome AF: 0.164 AC: 234334 AN: 1425730 Hom.: 20441 Cov.: 34 AF XY: 0.164 AC XY: 115860 AN XY: 704384

Gnomad4 AFR exome AF: 0.0495

Gnomad4 AMR exome AF: 0.0929

Gnomad4 ASJ exome AF: 0.0938

Gnomad4 EAS exome AF: 0.0382

Gnomad4 SAS exome AF: 0.166

Gnomad4 FIN exome AF: 0.112

Gnomad4 NFE exome AF: 0.180

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.125 AC: 18958 AN: 152172 Hom.: 1403 Cov.: 32 AF XY: 0.122 AC XY: 9076 AN XY: 74382

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0977

Gnomad4 EAS AF: 0.0425

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0937

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.146

Alfa AF: 0.146 Hom.: 446

Bravo AF: 0.121

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.8
Dann	Benign	0.58

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

Other links and lift over

dbSNP: rs73215937; hg19: chr3-132075759;