rs62638747

Variant names:

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001611.5(ACP5):c.225C>T(p.Phe75Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,613,984 control chromosomes in the GnomAD database, including 11,166 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.094 ( 827 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10339 hom. )

Consequence

ACP5
NM_001611.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 2.53

Variant links:

Genes affected

ACP5 (HGNC:124): (acid phosphatase 5, tartrate resistant) This gene encodes an iron containing glycoprotein which catalyzes the conversion of orthophosphoric monoester to alcohol and orthophosphate. It is the most basic of the acid phosphatases and is the only form not inhibited by L(+)-tartrate. [provided by RefSeq, Aug 2008]

ACP5 links:

ZNF627 (HGNC:30570): (zinc finger protein 627) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF627 links:

LOC124904638 (HGNC:):

LOC124904638 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 19-11577093-G-A is Benign according to our data. Variant chr19-11577093-G-A is described in ClinVar as [Benign]. Clinvar id is 257477.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.53 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACP5	NM_001611.5 link	c.225C>T	p.Phe75Phe	synonymous_variant	Exon 2 of 5	ENST00000648477.1	NP_001602.1	P13686A0A024R7F8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACP5	ENST00000648477.1 link	c.225C>T	p.Phe75Phe	synonymous_variant	Exon 2 of 5		NM_001611.5	ENSP00000496973.1		P13686

Frequencies

GnomAD3 genomes

AF:

0.0942

AC:

14327

AN:

152076

Hom.:

826

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0382

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.0819

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.0224

Gnomad SAS

AF:

0.0872

Gnomad FIN

AF:

0.156

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.112

GnomAD3 exomes

AF:

0.100

AC:

25254

AN:

251446

Hom.:

1518

AF XY:

0.104

AC XY:

14164

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.0383

Gnomad AMR exome

AF:

0.0648

Gnomad ASJ exome

AF:

0.123

Gnomad EAS exome

AF:

0.0206

Gnomad SAS exome

AF:

0.0937

Gnomad FIN exome

AF:

0.150

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.127

GnomAD4 exome

AF:

0.116

AC:

169407

AN:

1461790

Hom.:

10339

Cov.:

AF XY:

0.116

AC XY:

84295

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.0382

Gnomad4 AMR exome

AF:

0.0689

Gnomad4 ASJ exome

AF:

0.124

Gnomad4 EAS exome

AF:

0.0247

Gnomad4 SAS exome

AF:

0.0970

Gnomad4 FIN exome

AF:

0.150

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.112

GnomAD4 genome

AF:

0.0941

AC:

14327

AN:

152194

Hom.:

827

Cov.:

AF XY:

0.0937

AC XY:

6969

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.0381

Gnomad4 AMR

AF:

0.0818

Gnomad4 ASJ

AF:

0.124

Gnomad4 EAS

AF:

0.0226

Gnomad4 SAS

AF:

0.0866

Gnomad4 FIN

AF:

0.156

Gnomad4 NFE

AF:

0.124

Gnomad4 OTH

AF:

0.112

Alfa

AF:

0.113

Hom.:

547

Bravo

AF:

0.0873

Asia WGS

AF:

0.0630

AC:

218

AN:

3478

EpiCase

AF:

0.127

EpiControl

AF:

0.130

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 24% of patients studied by a panel of primary immunodeficiencies. Number of patients: 21. Only high quality variants are reported. -

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:2

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Spondyloenchondrodysplasia with immune dysregulation

Benign:2

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

9.8

DANN

Benign

0.65

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over