Genetic Variant ACP1:c.*812A>G (chr2-273070-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000405233.5(ACP1):c.*812A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 154,412 control chromosomes in the GnomAD database, including 64,445 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 0.91 ( 63563 hom., cov: 32)

Exomes 𝑓: 0.89 ( 882 hom. )

Consequence

ACP1
ENST00000405233.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.57

Publications

8 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.05).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ACP1	NM_004300.4 link	c.231+920A>G	intron_variant	Intron 3 of 5	ENST00000272065.10	NP_004291.1	P24666-1Q59EH3
ACP1	NM_007099.4 link	c.231+765A>G	intron_variant	Intron 3 of 5		NP_009030.1	P24666-2
ACP1	NR_024080.2 link	n.278+765A>G	intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACP1	ENST00000272065.10 link	c.231+920A>G		intron_variant	Intron 3 of 5	1	NM_004300.4	ENSP00000272065.5		P24666-1

Frequencies

GnomAD3 genomes

AF:

0.913

AC:

138849

AN:

152062

Hom.:

63510

Cov.:

show subpopulations

Gnomad AFR

AF:

0.968

Gnomad AMI

AF:

0.825

Gnomad AMR

AF:

0.893

Gnomad ASJ

AF:

0.885

Gnomad EAS

AF:

0.890

Gnomad SAS

AF:

0.920

Gnomad FIN

AF:

0.843

Gnomad MID

AF:

0.911

Gnomad NFE

AF:

0.899

Gnomad OTH

AF:

0.907

GnomAD4 exome

AF:

0.887

AC:

1979

AN:

2232

Hom.:

882

Cov.:

AF XY:

0.897

AC XY:

1003

AN XY:

1118

show subpopulations

African (AFR)

AF:

0.919

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.851

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

0.878

AC:

1435

AN:

1634

European-Non Finnish (NFE)

AF:

0.902

AC:

202

AN:

224

Other (OTH)

AF:

0.937

AC:

178

AN:

190

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

140

<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:

0.913

AC:

138959

AN:

152180

Hom.:

63563

Cov.:

AF XY:

0.910

AC XY:

67683

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.968

AC:

40190

AN:

41530

American (AMR)

AF:

0.893

AC:

13654

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.885

AC:

3072

AN:

3472

East Asian (EAS)

AF:

0.890

AC:

4582

AN:

5148

South Asian (SAS)

AF:

0.919

AC:

4411

AN:

4800

European-Finnish (FIN)

AF:

0.843

AC:

8938

AN:

10600

Middle Eastern (MID)

AF:

0.912

AC:

268

AN:

294

European-Non Finnish (NFE)

AF:

0.899

AC:

61176

AN:

68018

Other (OTH)

AF:

0.906

AC:

1916

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

618

1235

1853

2470

3088

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

904

1808

2712

3616

4520

<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:

0.914

Hom.:

11032

Bravo

AF:

0.920

Asia WGS

AF:

0.906

AC:

3147

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

1.4

(source)

DANN

Benign

0.32

PhyloP100

-1.6

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over