Variant 11-47247608-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001610.4(ACP2):c.297+33A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,612,838 control chromosomes in the GnomAD database, including 55,410 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 0.30 ( 8261 hom., cov: 33)

Exomes 𝑓: 0.23 ( 47149 hom. )

Consequence

ACP2
NM_001610.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00900

Variant links:

Genes affected

ACP2 (HGNC:123): (acid phosphatase 2, lysosomal) The protein encoded by this gene belongs to the histidine acid phosphatase family, which hydrolyze orthophosphoric monoesters to alcohol and phosphate. This protein is localized to the lysosomal membrane, and is chemically and genetically distinct from the red cell acid phosphatase. Mice lacking this gene showed multiple defects, including bone structure alterations, lysosomal storage defects, and an increased tendency towards seizures. An enzymatically-inactive allele of this gene in mice showed severe growth retardation, hair-follicle abnormalities, and an ataxia-like phenotype. Alternatively spliced transcript variants have been found for this gene. A C-terminally extended isoform is also predicted to be produced by the use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism. [provided by RefSeq, Oct 2017]

ACP2 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 (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACP2	NM_001610.4 linkuse as main transcript	c.297+33A>G		intron_variant		ENST00000672073.1	NP_001601.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACP2	ENST00000672073.1 linkuse as main transcript	c.297+33A>G		intron_variant			NM_001610.4	ENSP00000500291	P1	P11117-1

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45871

AN:

152030

Hom.:

8261

Cov.:

show subpopulations

Gnomad AFR

AF:

0.437

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.694

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.342

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.254

GnomAD3 exomes

AF:

0.302

AC:

76001

AN:

251358

Hom.:

14609

AF XY:

0.293

AC XY:

39746

AN XY:

135860

show subpopulations

Gnomad AFR exome

AF:

0.438

Gnomad AMR exome

AF:

0.400

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.708

Gnomad SAS exome

AF:

0.348

Gnomad FIN exome

AF:

0.332

Gnomad NFE exome

AF:

0.188

Gnomad OTH exome

AF:

0.226

GnomAD4 exome

AF:

0.231

AC:

336694

AN:

1460688

Hom.:

47149

Cov.:

AF XY:

0.232

AC XY:

168620

AN XY:

726736

show subpopulations

Gnomad4 AFR exome

AF:

0.443

Gnomad4 AMR exome

AF:

0.386

Gnomad4 ASJ exome

AF:

0.142

Gnomad4 EAS exome

AF:

0.690

Gnomad4 SAS exome

AF:

0.347

Gnomad4 FIN exome

AF:

0.316

Gnomad4 NFE exome

AF:

0.190

Gnomad4 OTH exome

AF:

0.243

GnomAD4 genome

AF:

0.302

AC:

45898

AN:

152150

Hom.:

8261

Cov.:

AF XY:

0.313

AC XY:

23278

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.436

Gnomad4 AMR

AF:

0.291

Gnomad4 ASJ

AF:

0.147

Gnomad4 EAS

AF:

0.694

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.342

Gnomad4 NFE

AF:

0.195

Gnomad4 OTH

AF:

0.251

Alfa

AF:

0.176

Hom.:

647

Bravo

AF:

0.304

Asia WGS

AF:

0.466

AC:

1618

AN:

3478

EpiCase

AF:

0.178

EpiControl

AF:

0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.4

DANN

Benign

0.45

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