dbSNP rs11553746: ACP1:p.Thr95Ile (chr2-272203-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001040649.3(ACP1):c.284C>T(p.Thr95Ile) variant causes a missense change. The variant allele was found at a frequency of 0.328 in 1,613,824 control chromosomes in the GnomAD database, including 89,201 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 0.28 ( 6477 hom., cov: 32)

Exomes 𝑓: 0.33 ( 82724 hom. )

Consequence

ACP1
NM_001040649.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.74

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016343594).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACP1	NM_004300.4 link	c.231+53C>T		intron_variant	Intron 3 of 5	ENST00000272065.10	NP_004291.1	P24666-1Q59EH3
ACP1	NM_001040649.3 link	c.284C>T	p.Thr95Ile	missense_variant	Exon 3 of 3		NP_001035739.1	A0A140VK37
ACP1	NM_007099.4 link	c.129C>T	p.Asp43Asp	synonymous_variant	Exon 3 of 6		NP_009030.1	P24666-2
ACP1	NR_024080.2 link	n.176C>T		non_coding_transcript_exon_variant	Exon 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACP1	ENST00000272065.10 link	c.231+53C>T		intron_variant	Intron 3 of 5	1	NM_004300.4	ENSP00000272065.5		P24666-1

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42417

AN:

151960

Hom.:

6481

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.441

Gnomad AMR

AF:

0.248

Gnomad ASJ

AF:

0.271

Gnomad EAS

AF:

0.236

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.361

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.248

GnomAD3 exomes

AF:

0.305

AC:

76731

AN:

251206

Hom.:

12172

AF XY:

0.310

AC XY:

42076

AN XY:

135760

show subpopulations

Gnomad AFR exome

AF:

0.161

Gnomad AMR exome

AF:

0.249

Gnomad ASJ exome

AF:

0.272

Gnomad EAS exome

AF:

0.229

Gnomad SAS exome

AF:

0.307

Gnomad FIN exome

AF:

0.366

Gnomad NFE exome

AF:

0.347

Gnomad OTH exome

AF:

0.303

GnomAD4 exome

AF:

0.333

AC:

486159

AN:

1461746

Hom.:

82724

Cov.:

AF XY:

0.333

AC XY:

241899

AN XY:

727160

show subpopulations

Gnomad4 AFR exome

AF:

0.149

Gnomad4 AMR exome

AF:

0.246

Gnomad4 ASJ exome

AF:

0.269

Gnomad4 EAS exome

AF:

0.221

Gnomad4 SAS exome

AF:

0.312

Gnomad4 FIN exome

AF:

0.365

Gnomad4 NFE exome

AF:

0.349

Gnomad4 OTH exome

AF:

0.310

GnomAD4 genome

AF:

0.279

AC:

42408

AN:

152078

Hom.:

6477

Cov.:

AF XY:

0.280

AC XY:

20834

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.248

Gnomad4 ASJ

AF:

0.271

Gnomad4 EAS

AF:

0.235

Gnomad4 SAS

AF:

0.298

Gnomad4 FIN

AF:

0.361

Gnomad4 NFE

AF:

0.346

Gnomad4 OTH

AF:

0.245

Alfa

AF:

0.324

Hom.:

13034

Bravo

AF:

0.262

TwinsUK

AF:

0.346

AC:

1284

ALSPAC

AF:

0.336

AC:

1295

ESP6500AA

AF:

0.170

AC:

749

ESP6500EA

AF:

0.345

AC:

2963

ExAC

AF:

0.310

AC:

37609

Asia WGS

AF:

0.266

AC:

925

AN:

3478

EpiCase

AF:

0.333

EpiControl

AF:

0.328

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.41

BayesDel_noAF

Benign

-0.22

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0046

.;T

Eigen

Pathogenic

0.74

Eigen_PC

Pathogenic

0.76

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.45

T;.

MetaRNN

Benign

0.0016

T;T

MetaSVM

Benign

-1.1

PROVEAN

Benign

-0.13

N;N

REVEL

Benign

0.14

Sift

Uncertain

0.018

D;T

Sift4G

Benign

0.17

T;T

Vest4

0.66

ClinPred

0.046

GERP RS

5.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.15

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over