2-273070-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACP1	NM_004300.4	c.231+920A>G		intron_variant	Intron 3 of 5	ENST00000272065.10	NP_004291.1
ACP1	NM_007099.4	c.231+765A>G		intron_variant	Intron 3 of 5		NP_009030.1
ACP1	NR_024080.2	n.278+765A>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACP1	ENST00000272065.10	c.231+920A>G		intron_variant	Intron 3 of 5	1	NM_004300.4	ENSP00000272065.5

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

Gnomad4 AFR exome AF: 0.919

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 SAS exome AF: 0.851

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.902

Gnomad4 OTH exome AF: 0.937

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

Gnomad4 AFR AF: 0.968

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.843

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.906

Alfa AF: 0.912 Hom.: 10664

Bravo AF: 0.920

Asia WGS AF: 0.906 AC: 3147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.32

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: rs12714403; hg19: chr2-273070;