rs73215937

Variant names:

• chr3-132356915-T-C
• rs73215937
• NM_001099.5:c.*37T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ACP3	NM_001099.5	c.*37T>C		3_prime_UTR_variant	Exon 10 of 10	ENST00000336375.10	NP_001090.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACP3	ENST00000336375.10	c.*37T>C		3_prime_UTR_variant	Exon 10 of 10	1	NM_001099.5	ENSP00000337471.5
ACP3	ENST00000475741.5	c.*37T>C		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000417744.1
ACP3	ENST00000351273.12	c.1138+60T>C		intron_variant	Intron 10 of 10	1		ENSP00000323036.8
ACP3	ENST00000507647.1	c.190+60T>C		intron_variant	Intron 2 of 2	5		ENSP00000422036.1

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

GnomAD2 exomes AF: 0.131 AC: 30525 AN: 232388 AF XY: 0.137

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 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

African (AFR) AF: 0.0495 AC: 1601 AN: 32338

American (AMR) AF: 0.0929 AC: 3683 AN: 39662

Ashkenazi Jewish (ASJ) AF: 0.0938 AC: 2345 AN: 24992

East Asian (EAS) AF: 0.0382 AC: 1482 AN: 38820

South Asian (SAS) AF: 0.166 AC: 13763 AN: 82698

European-Finnish (FIN) AF: 0.112 AC: 5922 AN: 52940

Middle Eastern (MID) AF: 0.132 AC: 744 AN: 5628

European-Non Finnish (NFE) AF: 0.180 AC: 195770 AN: 1089912

Other (OTH) AF: 0.154 AC: 9024 AN: 58740

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

African (AFR) AF: 0.0586 AC: 2433 AN: 41524

American (AMR) AF: 0.120 AC: 1833 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0977 AC: 339 AN: 3470

East Asian (EAS) AF: 0.0425 AC: 220 AN: 5174

South Asian (SAS) AF: 0.146 AC: 703 AN: 4820

European-Finnish (FIN) AF: 0.0937 AC: 992 AN: 10590

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11952 AN: 67990

Other (OTH) AF: 0.146 AC: 308 AN: 2112

Alfa AF: 0.152 Hom.: 2770

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
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: rs73215937; hg19: chr3-132075759;