chr2-54054625-C-T

Position:

• chr2-54054625-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.156-2614C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 152,010 control chromosomes in the GnomAD database, including 23,981 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 0.56 (23981 hom., cov: 32)
• Consequence: ACYP2 NM_001320586.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACYP2	NM_001320586.2	c.156-2614C>T		intron_variant		ENST00000607452.6	NP_001307515.1
ACYP2	NM_001320587.2	c.63-2614C>T		intron_variant			NP_001307516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACYP2	ENST00000607452.6	c.156-2614C>T		intron_variant		2	NM_001320586.2	ENSP00000475986
ACYP2	ENST00000422521.2	c.156-2614C>T		intron_variant		5		ENSP00000475658
ACYP2	ENST00000458030.3	n.676-2614C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84657 AN: 151892 Hom.: 23949 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.557 AC: 84738 AN: 152010 Hom.: 23981 Cov.: 32 AF XY: 0.563 AC XY: 41859 AN XY: 74310

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.535

Alfa AF: 0.502 Hom.: 25603

Bravo AF: 0.551

Asia WGS AF: 0.698 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1363062; hg19: chr2-54281762;