rs860056

Positions:

• chr2-54284089-T-C
• chr2-54284089-T-G

Variant summary

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

The NM_001320586.2(ACYP2):​c.405-20599T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,108 control chromosomes in the GnomAD database, including 22,720 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 0.53 (22720 hom., cov: 33)
• Consequence: ACYP2 NM_001320586.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

ACYP2 (HGNC:180): (acylphosphatase 2) Acylphosphatase can hydrolyze the phosphoenzyme intermediate of different membrane pumps, particularly the Ca2+/Mg2+-ATPase from sarcoplasmic reticulum of skeletal muscle. Two isoenzymes have been isolated, called muscle acylphosphatase and erythrocyte acylphosphatase on the basis of their tissue localization. This gene encodes the muscle-type isoform (MT). An increase of the MT isoform is associated with muscle differentiation. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACYP2	NM_001320586.2	c.405-20599T>C		intron_variant		ENST00000607452.6	NP_001307515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACYP2	ENST00000607452.6	c.405-20599T>C		intron_variant		2	NM_001320586.2	ENSP00000475986.1
ACYP2	ENST00000394666.8	c.186-20599T>C		intron_variant		1		ENSP00000378161.3

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80978 AN: 151990 Hom.: 22669 Cov.: 33

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.533 AC: 81088 AN: 152108 Hom.: 22720 Cov.: 33 AF XY: 0.526 AC XY: 39138 AN XY: 74366

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.529

Alfa AF: 0.385 Hom.: 1421

Bravo AF: 0.562

Asia WGS AF: 0.385 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.44

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: rs860056; hg19: chr2-54511226;