Genetic Variant ACP3:c.*829T>C (chr3-132357707-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001099.5(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
NM_001099.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.254

Publications

6 publications found

Variant links:

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]

ACP3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACP3	NM_001099.5	MANE Select	c.*829T>C	3_prime_UTR	Exon 10 of 10	NP_001090.2
ACP3	NM_001292037.2		c.*829T>C	3_prime_UTR	Exon 9 of 9	NP_001278966.1
ACP3	NM_001134194.2		c.1138+852T>C	intron	N/A	NP_001127666.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ACP3	ENST00000336375.10	TSL:1 MANE Select	c.*829T>C	3_prime_UTR	Exon 10 of 10	ENSP00000337471.5
ACP3	ENST00000351273.12	TSL:1	c.1138+852T>C	intron	N/A	ENSP00000323036.8
ACP3	ENST00000507647.1	TSL:5	c.191-710T>C	intron	N/A	ENSP00000422036.1

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

72378

AN:

151800

Hom.:

18027

Cov.:

show subpopulations

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.:

AF XY:

0.574

AC XY:

220884

AN XY:

384650

show subpopulations

African (AFR)

AF:

0.353

AC:

5564

AN:

15782

American (AMR)

AF:

0.461

AC:

454

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.569

AC:

2931

AN:

5152

East Asian (EAS)

AF:

0.126

AC:

458

AN:

3628

South Asian (SAS)

AF:

0.547

AC:

9001

AN:

16454

European-Finnish (FIN)

AF:

0.388

AC:

108

AN:

278

Middle Eastern (MID)

AF:

0.588

AC:

952

AN:

1618

European-Non Finnish (NFE)

AF:

0.582

AC:

443439

AN:

761758

Other (OTH)

AF:

0.547

AC:

14939

AN:

27292

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

10310

20620

30931

41241

51551

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16612

33224

49836

66448

83060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.476

AC:

72387

AN:

151918

Hom.:

18028

Cov.:

AF XY:

0.468

AC XY:

34766

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.379

AC:

15688

AN:

41430

American (AMR)

AF:

0.485

AC:

7386

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.555

AC:

1925

AN:

3470

East Asian (EAS)

AF:

0.122

AC:

628

AN:

5164

South Asian (SAS)

AF:

0.514

AC:

2470

AN:

4810

European-Finnish (FIN)

AF:

0.360

AC:

3795

AN:

10534

Middle Eastern (MID)

AF:

0.653

AC:

192

AN:

294

European-Non Finnish (NFE)

AF:

0.568

AC:

38589

AN:

67948

Other (OTH)

AF:

0.503

AC:

1063

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1862

3724

5586

7448

9310

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.539

Hom.:

28787

Bravo

AF:

0.475

Asia WGS

AF:

0.306

AC:

1066

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.6

(source)

DANN

Benign

0.39

PhyloP100

-0.25

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over