rs12714402

chr2-272926-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

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]

ACMG classification

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 = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACP1	NM_004300.4	c.231+776A>G		intron_variant		ENST00000272065.10
ACP1	NM_007099.4	c.231+621A>G		intron_variant
ACP1	NR_024080.2	n.278+621A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACP1	ENST00000272065.10	c.231+776A>G		intron_variant		1	NM_004300.4	P3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93582 AN: 151954 Hom.: 29870 Cov.: 33

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.: 0 AF XY: 0.534 AC XY: 610 AN XY: 1142

Gnomad4 AFR exome AF: 0.378

Gnomad4 AMR exome AF: 0.444

Gnomad4 ASJ exome AF: 1.00

Gnomad4 SAS exome AF: 0.564

Gnomad4 NFE exome AF: 0.670

Gnomad4 OTH exome AF: 0.577

GnomAD4 genome AF: 0.615 AC: 93598 AN: 152072 Hom.: 29865 Cov.: 33 AF XY: 0.619 AC XY: 46023 AN XY: 74346

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.574

Alfa AF: 0.668 Hom.: 37880

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
Dann	Benign	0.49

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

Other links and lift over

dbSNP: rs12714402; hg19: chr2-272926;