3-132357707-T-C

Position:

• chr3-132357707-T-C

Variant summary

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

The ENST00000336375.10(ACP3):​c.*829T>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 0.559 in 984,864 control chromosomes in the GnomAD database, including 156,048 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 0.48 (18028 hom., cov: 30)
  • Exomes 𝑓: 0.57 (138020 hom.)
• Consequence: ACP3 ENST00000336375.10 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACP3	NM_001099.5	c.*829T>C		3_prime_UTR_variant	10/10	ENST00000336375.10	NP_001090.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACP3	ENST00000336375.10	c.*829T>C		3_prime_UTR_variant	10/10	1	NM_001099.5	ENSP00000337471
ACP3	ENST00000351273.12	c.1138+852T>C		intron_variant		1		ENSP00000323036	P1
ACP3	ENST00000507647.1	c.193-710T>C		intron_variant		5		ENSP00000422036

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72378 AN: 151800 Hom.: 18027 Cov.: 30

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.508

GnomAD4 exome AF: 0.574 AC: 477846 AN: 832946 Hom.: 138020 Cov.: 34 AF XY: 0.574 AC XY: 220884 AN XY: 384650

Gnomad4 AFR exome AF: 0.353

Gnomad4 AMR exome AF: 0.461

Gnomad4 ASJ exome AF: 0.569

Gnomad4 EAS exome AF: 0.126

Gnomad4 SAS exome AF: 0.547

Gnomad4 FIN exome AF: 0.388

Gnomad4 NFE exome AF: 0.582

Gnomad4 OTH exome AF: 0.547

GnomAD4 genome AF: 0.476 AC: 72387 AN: 151918 Hom.: 18028 Cov.: 30 AF XY: 0.468 AC XY: 34766 AN XY: 74246

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.503

Alfa AF: 0.546 Hom.: 22640

Bravo AF: 0.475

Asia WGS AF: 0.306 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.39

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: rs14192; hg19: chr3-132076551;