2-266907-C-G

Variant names:

• chr2-266907-C-G
• rs10171111
• NM_004300.4:c.43+1900C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ACP1	NM_004300.4	c.43+1900C>G		intron_variant	Intron 1 of 5	ENST00000272065.10	NP_004291.1
ACP1	NM_007099.4	c.43+1900C>G		intron_variant	Intron 1 of 5		NP_009030.1
ACP1	NM_001040649.3	c.43+1900C>G		intron_variant	Intron 1 of 2		NP_001035739.1
ACP1	NR_024080.2	n.61+1900C>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACP1	ENST00000272065.10	c.43+1900C>G		intron_variant	Intron 1 of 5	1	NM_004300.4	ENSP00000272065.5

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

African (AFR) AF: 0.468 AC: 19332 AN: 41334

American (AMR) AF: 0.529 AC: 8081 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2075 AN: 3468

East Asian (EAS) AF: 0.827 AC: 4270 AN: 5162

South Asian (SAS) AF: 0.572 AC: 2746 AN: 4804

European-Finnish (FIN) AF: 0.760 AC: 8027 AN: 10560

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46977 AN: 67974

Other (OTH) AF: 0.574 AC: 1205 AN: 2100

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
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10171111; hg19: chr2-266907;