rs1559040

chr2-54120613-C-T

Variant summary

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

The NM_001320586.2(ACYP2):c.278-14840C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,228 control chromosomes in the GnomAD database, including 979 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 0.11 (979 hom., cov: 32)
• Consequence: ACYP2 NM_001320586.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACYP2	NM_001320586.2	c.278-14840C>T		intron_variant		ENST00000607452.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACYP2	ENST00000607452.6	c.278-14840C>T		intron_variant		2	NM_001320586.2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16785 AN: 152110 Hom.: 977 Cov.: 32

Gnomad AFR AF: 0.0926

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.110 AC: 16801 AN: 152228 Hom.: 979 Cov.: 32 AF XY: 0.109 AC XY: 8101 AN XY: 74438

Gnomad4 AFR AF: 0.0928

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0681

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.0993

Alfa AF: 0.0641 Hom.: 201

Bravo AF: 0.111

Asia WGS AF: 0.0430 AC: 151 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	0.50
Dann	Benign	0.36

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: rs1559040; hg19: chr2-54347750;