2-266907-C-G

Variant summary

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

The NM_004300.4(ACP1):c.43+1900C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,870 control chromosomes in the GnomAD database, including 29,838 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 (29838 hom., cov: 31)
• Consequence: ACP1 NM_004300.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

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=-0.98).
• 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.43+1900C>G		intron_variant		ENST00000272065.10
ACP1	NM_001040649.3	c.43+1900C>G		intron_variant
ACP1	NM_007099.4	c.43+1900C>G		intron_variant
ACP1	NR_024080.2	n.61+1900C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACP1	ENST00000272065.10	c.43+1900C>G		intron_variant		1	NM_004300.4	P3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93507 AN: 151752 Hom.: 29842 Cov.: 31

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: 0.573

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.577

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.616 AC: 93524 AN: 151870 Hom.: 29838 Cov.: 31 AF XY: 0.620 AC XY: 45995 AN XY: 74218

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.574

Alfa AF: 0.647 Hom.: 3847

Bravo AF: 0.590

Asia WGS AF: 0.644 AC: 2240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.1
Dann	Benign	0.26

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: rs10171111; hg19: chr2-266907;