chr2-273070-A-G

Variant names:

• chr2-273070-A-G
• rs12714403
• ENST00000405233.5:c.*812A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000405233.5(ACP1):​c.*812A>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 0.913 in 154,412 control chromosomes in the GnomAD database, including 64,445 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 0.91 (63563 hom., cov: 32)
  • Exomes 𝑓: 0.89 (882 hom.)
• Consequence: ACP1 ENST00000405233.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 8 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000405233.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACP1	NM_004300.4	MANE Select	c.231+920A>G		intron	N/A	NP_004291.1	P24666-1
	ACP1	NM_007099.4		c.231+765A>G		intron	N/A	NP_009030.1	P24666-2
	ACP1	NR_024080.2		n.278+765A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACP1	ENST00000405233.5	TSL:1	c.*812A>G		3_prime_UTR	Exon 4 of 4	ENSP00000384307.1	F2Z2Q9
	ACP1	ENST00000272065.10	TSL:1 MANE Select	c.231+920A>G		intron	N/A	ENSP00000272065.5	P24666-1
	ACP1	ENST00000272067.11	TSL:1	c.231+765A>G		intron	N/A	ENSP00000272067.6	P24666-2

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138849 AN: 152062 Hom.: 63510 Cov.: 32

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.907

GnomAD4 exome AF: 0.887 AC: 1979 AN: 2232 Hom.: 882 Cov.: 0 AF XY: 0.897 AC XY: 1003 AN XY: 1118

African (AFR) AF: 0.919 AC: 68 AN: 74

American (AMR) AF: 1.00 AC: 8 AN: 8

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 4 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.851 AC: 80 AN: 94

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AF: 0.878 AC: 1435 AN: 1634

European-Non Finnish (NFE) AF: 0.902 AC: 202 AN: 224

Other (OTH) AF: 0.937 AC: 178 AN: 190

GnomAD4 genome AF: 0.913 AC: 138959 AN: 152180 Hom.: 63563 Cov.: 32 AF XY: 0.910 AC XY: 67683 AN XY: 74378

African (AFR) AF: 0.968 AC: 40190 AN: 41530

American (AMR) AF: 0.893 AC: 13654 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3072 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4582 AN: 5148

South Asian (SAS) AF: 0.919 AC: 4411 AN: 4800

European-Finnish (FIN) AF: 0.843 AC: 8938 AN: 10600

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61176 AN: 68018

Other (OTH) AF: 0.906 AC: 1916 AN: 2114

Alfa AF: 0.914 Hom.: 11032

Bravo AF: 0.920

Asia WGS AF: 0.906 AC: 3147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.32
PhyloP100		-1.6
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: rs12714403; hg19: chr2-273070;