2-277003-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_004300.4(ACP1):c.317A>G(p.Gln106Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,598,632 control chromosomes in the GnomAD database, including 89,383 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 6943 hom., cov: 33)

Exomes 𝑓: 0.33 ( 82440 hom. )

Consequence

ACP1
NM_004300.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 2.79

Publications

43 publications found

Variant links:

Genes affected

ACP1 (HGNC:122): (acid phosphatase 1) The product of this gene belongs to the phosphotyrosine protein phosphatase family of proteins. It functions as an acid phosphatase and a protein tyrosine phosphatase by hydrolyzing protein tyrosine phosphate to protein tyrosine and orthophosphate. This enzyme also hydrolyzes orthophosphoric monoesters to alcohol and orthophosphate. This gene is genetically polymorphic, and three common alleles segregating at the corresponding locus give rise to six phenotypes. Each allele appears to encode at least two electrophoretically different isozymes, Bf and Bs, which are produced in allele-specific ratios. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Aug 2008]

ACP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.003926754).

BP6

Variant 2-277003-A-G is Benign according to our data. Variant chr2-277003-A-G is described in ClinVar as Benign. ClinVar VariationId is 13685.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004300.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ACP1	NM_004300.4	MANE Select	c.317A>G	p.Gln106Arg	missense	Exon 5 of 6	NP_004291.1
ACP1	NM_007099.4		c.317A>G	p.Gln106Arg	missense	Exon 5 of 6	NP_009030.1
ACP1	NR_024080.2		n.364A>G		non_coding_transcript_exon	Exon 6 of 7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ACP1	ENST00000272065.10	TSL:1 MANE Select	c.317A>G	p.Gln106Arg	missense	Exon 5 of 6	ENSP00000272065.5
ACP1	ENST00000272067.11	TSL:1	c.317A>G	p.Gln106Arg	missense	Exon 5 of 6	ENSP00000272067.6
ACP1	ENST00000453390.5	TSL:1	n.*133A>G		non_coding_transcript_exon	Exon 6 of 7	ENSP00000411121.1

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44899

AN:

152026

Hom.:

6950

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.440

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.271

Gnomad EAS

AF:

0.234

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.361

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.261

GnomAD2 exomes

AF:

0.310

AC:

76287

AN:

245720

AF XY:

0.314

show subpopulations

Gnomad AFR exome

AF:

0.221

Gnomad AMR exome

AF:

0.252

Gnomad ASJ exome

AF:

0.272

Gnomad EAS exome

AF:

0.229

Gnomad FIN exome

AF:

0.366

Gnomad NFE exome

AF:

0.347

Gnomad OTH exome

AF:

0.304

GnomAD4 exome

AF:

0.333

AC:

482181

AN:

1446486

Hom.:

82440

Cov.:

AF XY:

0.333

AC XY:

239998

AN XY:

719940

show subpopulations

African (AFR)

AF:

0.206

AC:

6786

AN:

32882

American (AMR)

AF:

0.249

AC:

10836

AN:

43586

Ashkenazi Jewish (ASJ)

AF:

0.268

AC:

6948

AN:

25900

East Asian (EAS)

AF:

0.222

AC:

8791

AN:

39652

South Asian (SAS)

AF:

0.312

AC:

26340

AN:

84370

European-Finnish (FIN)

AF:

0.365

AC:

19459

AN:

53362

Middle Eastern (MID)

AF:

0.264

AC:

1279

AN:

4846

European-Non Finnish (NFE)

AF:

0.348

AC:

383018

AN:

1102116

Other (OTH)

AF:

0.313

AC:

18724

AN:

59772

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

13867

27735

41602

55470

69337

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12118

24236

36354

48472

60590

<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:

0.295

AC:

44897

AN:

152146

Hom.:

6943

Cov.:

AF XY:

0.296

AC XY:

22035

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.218

AC:

9051

AN:

41508

American (AMR)

AF:

0.252

AC:

3853

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.271

AC:

942

AN:

3470

East Asian (EAS)

AF:

0.234

AC:

1210

AN:

5170

South Asian (SAS)

AF:

0.299

AC:

1440

AN:

4822

European-Finnish (FIN)

AF:

0.361

AC:

3816

AN:

10570

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.347

AC:

23569

AN:

67998

Other (OTH)

AF:

0.258

AC:

546

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1633

3266

4899

6532

8165

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<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:

0.318

Hom.:

12824

Bravo

AF:

0.281

TwinsUK

AF:

0.347

AC:

1287

ALSPAC

AF:

0.336

AC:

1296

ESP6500AA

AF:

0.223

AC:

983

ESP6500EA

AF:

0.344

AC:

2959

ExAC

AF:

0.315

AC:

38242

Asia WGS

AF:

0.270

AC:

939

AN:

3478

EpiCase

AF:

0.334

EpiControl

AF:

0.328

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

ACP1 A/B POLYMORPHISM

Benign:1

Jan 07, 2025

OMIM

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:literature only

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.41

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.041

Eigen

Benign

-0.44

Eigen_PC

Benign

-0.24

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.56

MetaRNN

Benign

0.0039

MetaSVM

Benign

-0.89

MutationAssessor

Benign

-0.19

PhyloP100

2.8

PrimateAI

Benign

0.42

PROVEAN

Benign

-0.92

REVEL

Benign

0.27

Sift

Benign

0.18

Sift4G

Benign

0.20

Polyphen

0.0

Vest4

0.11

MPC

0.053

ClinPred

0.0041

GERP RS

3.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.24

gMVP

0.16

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over