NM_001099.5:c.969-1494G>A

Variant names:

• chr3-132355192-G-A
• rs9790142
• NM_001099.5:c.969-1494G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001099.5(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 NM_001099.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 1 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 = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACP3	NM_001099.5	c.969-1494G>A		intron_variant	Intron 9 of 9	ENST00000336375.10	NP_001090.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACP3	ENST00000336375.10	c.969-1494G>A		intron_variant	Intron 9 of 9	1	NM_001099.5	ENSP00000337471.5
ACP3	ENST00000351273.12	c.969-1494G>A		intron_variant	Intron 9 of 10	1		ENSP00000323036.8
ACP3	ENST00000475741.5	c.870-1494G>A		intron_variant	Intron 8 of 8	1		ENSP00000417744.1
ACP3	ENST00000507647.1	c.21-1494G>A		intron_variant	Intron 1 of 2	5		ENSP00000422036.1

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

African (AFR) AF: 0.267 AC: 11075 AN: 41486

American (AMR) AF: 0.356 AC: 5445 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3470

East Asian (EAS) AF: 0.0787 AC: 409 AN: 5194

South Asian (SAS) AF: 0.367 AC: 1770 AN: 4822

European-Finnish (FIN) AF: 0.268 AC: 2828 AN: 10560

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26607 AN: 67998

Other (OTH) AF: 0.348 AC: 734 AN: 2108

Alfa AF: 0.358 Hom.: 1698

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
PhyloP100		-0.19
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: rs9790142; hg19: chr3-132074036;