Genetic Variant ENST00000405233.5:c.*668A>G (chr2-272926-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.*668A>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 0.614 in 154,370 control chromosomes in the GnomAD database, including 30,202 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 0.62 ( 29865 hom., cov: 33)

Exomes 𝑓: 0.53 ( 337 hom. )

Consequence

ACP1
ENST00000405233.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.112

Publications

14 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:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ACP1	NM_004300.4 link	c.231+776A>G	intron_variant	Intron 3 of 5	ENST00000272065.10	NP_004291.1	P24666-1Q59EH3
ACP1	NM_007099.4 link	c.231+621A>G	intron_variant	Intron 3 of 5		NP_009030.1	P24666-2
ACP1	NR_024080.2 link	n.278+621A>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+776A>G		intron_variant	Intron 3 of 5	1	NM_004300.4	ENSP00000272065.5		P24666-1

Frequencies

GnomAD3 genomes

AF:

0.616

AC:

93582

AN:

151954

Hom.:

29870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.468

Gnomad AMI

AF:

0.697

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.598

Gnomad EAS

AF:

0.827

Gnomad SAS

AF:

0.571

Gnomad FIN

AF:

0.759

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.691

Gnomad OTH

AF:

0.577

GnomAD4 exome

AF:

0.535

AC:

1229

AN:

2298

Hom.:

337

Cov.:

AF XY:

0.534

AC XY:

610

AN XY:

1142

show subpopulations

African (AFR)

AF:

0.378

AC:

AN:

American (AMR)

AF:

0.444

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.564

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.512

AC:

835

AN:

1632

European-Non Finnish (NFE)

AF:

0.670

AC:

189

AN:

282

Other (OTH)

AF:

0.577

AC:

112

AN:

194

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

119

149

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<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:

0.615

AC:

93598

AN:

152072

Hom.:

29865

Cov.:

AF XY:

0.619

AC XY:

46023

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.468

AC:

19389

AN:

41472

American (AMR)

AF:

0.529

AC:

8088

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.598

AC:

2075

AN:

3468

East Asian (EAS)

AF:

0.827

AC:

4273

AN:

5166

South Asian (SAS)

AF:

0.569

AC:

2741

AN:

4818

European-Finnish (FIN)

AF:

0.759

AC:

8034

AN:

10584

Middle Eastern (MID)

AF:

0.602

AC:

177

AN:

294

European-Non Finnish (NFE)

AF:

0.691

AC:

46975

AN:

67968

Other (OTH)

AF:

0.574

AC:

1212

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1774

3548

5321

7095

8869

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

768

1536

2304

3072

3840

<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:

0.658

Hom.:

46296

Bravo

AF:

0.590

Asia WGS

AF:

0.645

AC:

2242

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.38

(source)

DANN

Benign

0.49

PhyloP100

-0.11

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