rs9790142

Positions:

• chr3-132355192-G-A

Variant summary

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

The ENST00000336375.10(ACP3):​c.969-1494G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,122 control chromosomes in the GnomAD database, including 9,070 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 0.34 (9070 hom., cov: 32)
• Consequence: ACP3 ENST00000336375.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

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 = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACP3	NM_001099.5	c.969-1494G>A		intron_variant		ENST00000336375.10	NP_001090.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACP3	ENST00000336375.10	c.969-1494G>A		intron_variant		1	NM_001099.5	ENSP00000337471
ACP3	ENST00000351273.12	c.969-1494G>A		intron_variant		1		ENSP00000323036	P1
ACP3	ENST00000475741.5	c.870-1494G>A		intron_variant		1		ENSP00000417744
ACP3	ENST00000507647.1	c.23-1494G>A		intron_variant		5		ENSP00000422036

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51121 AN: 152004 Hom.: 9068 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.336 AC: 51116 AN: 152122 Hom.: 9070 Cov.: 32 AF XY: 0.331 AC XY: 24632 AN XY: 74376

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.0787

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.348

Alfa AF: 0.361 Hom.: 1666

Bravo AF: 0.336

Asia WGS AF: 0.212 AC: 738 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	2.3
DANN	Benign	0.68

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: rs9790142; hg19: chr3-132074036;