Variant chr2-272051-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_004300.4(ACP1):c.132C>T(p.Ser44Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0468 in 1,613,538 control chromosomes in the GnomAD database, including 2,083 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 0.039 ( 180 hom., cov: 32)

Exomes 𝑓: 0.048 ( 1903 hom. )

Consequence

ACP1
NM_004300.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.07

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.26).

BP7

Synonymous conserved (PhyloP=3.07 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACP1	NM_004300.4 link	c.132C>T	p.Ser44Ser	synonymous_variant	3/6	ENST00000272065.10	NP_004291.1	P24666-1Q59EH3
ACP1	NM_001040649.3 link	c.132C>T	p.Ser44Ser	synonymous_variant	3/3		NP_001035739.1	A0A140VK37
ACP1	NM_007099.4 link	c.117+112C>T		intron_variant			NP_009030.1	P24666-2
ACP1	NR_024080.2 link	n.150C>T		non_coding_transcript_exon_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACP1	ENST00000272065.10 link	c.132C>T	p.Ser44Ser	synonymous_variant	3/6	1	NM_004300.4	ENSP00000272065.5		P24666-1

Frequencies

GnomAD3 genomes

AF:

0.0391

AC:

5930

AN:

151672

Hom.:

180

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00867

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.0318

Gnomad ASJ

AF:

0.0274

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00725

Gnomad FIN

AF:

0.0957

Gnomad MID

AF:

0.0350

Gnomad NFE

AF:

0.0557

Gnomad OTH

AF:

0.0325

GnomAD3 exomes

AF:

0.0392

AC:

9844

AN:

251366

Hom.:

302

AF XY:

0.0398

AC XY:

5413

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.00744

Gnomad AMR exome

AF:

0.0201

Gnomad ASJ exome

AF:

0.0291

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00549

Gnomad FIN exome

AF:

0.0856

Gnomad NFE exome

AF:

0.0571

Gnomad OTH exome

AF:

0.0372

GnomAD4 exome

AF:

0.0476

AC:

69571

AN:

1461782

Hom.:

1903

Cov.:

AF XY:

0.0471

AC XY:

34256

AN XY:

727192

show subpopulations

Gnomad4 AFR exome

AF:

0.00762

Gnomad4 AMR exome

AF:

0.0211

Gnomad4 ASJ exome

AF:

0.0286

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00618

Gnomad4 FIN exome

AF:

0.0842

Gnomad4 NFE exome

AF:

0.0539

Gnomad4 OTH exome

AF:

0.0418

GnomAD4 genome

AF:

0.0391

AC:

5930

AN:

151756

Hom.:

180

Cov.:

AF XY:

0.0404

AC XY:

2994

AN XY:

74080

show subpopulations

Gnomad4 AFR

AF:

0.00865

Gnomad4 AMR

AF:

0.0318

Gnomad4 ASJ

AF:

0.0274

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00748

Gnomad4 FIN

AF:

0.0957

Gnomad4 NFE

AF:

0.0557

Gnomad4 OTH

AF:

0.0322

Alfa

AF:

0.0484

Hom.:

Bravo

AF:

0.0336

Asia WGS

AF:

0.00433

AC:

AN:

3478

EpiCase

AF:

0.0562

EpiControl

AF:

0.0545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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