chr2-54054625-C-T

Variant names:

• chr2-54054625-C-T
• rs1363062
• NM_001320586.2:c.156-2614C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ACYP2	NM_001320586.2	c.156-2614C>T		intron_variant	Intron 3 of 6		NP_001307515.1
ACYP2	NM_001320587.2	c.63-2614C>T		intron_variant	Intron 2 of 5		NP_001307516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACYP2	ENST00000607452.6	c.156-2614C>T		intron_variant	Intron 3 of 6	2		ENSP00000475986.1
ACYP2	ENST00000422521.2	c.156-2614C>T		intron_variant	Intron 3 of 4	5		ENSP00000475658.1
ACYP2	ENST00000458030.3	n.676-2614C>T		intron_variant	Intron 3 of 4	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

African (AFR) AF: 0.636 AC: 26368 AN: 41474

American (AMR) AF: 0.490 AC: 7469 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1845 AN: 3468

East Asian (EAS) AF: 0.716 AC: 3700 AN: 5166

South Asian (SAS) AF: 0.626 AC: 3012 AN: 4812

European-Finnish (FIN) AF: 0.618 AC: 6518 AN: 10552

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34031 AN: 67968

Other (OTH) AF: 0.535 AC: 1128 AN: 2110

Alfa AF: 0.506 Hom.: 32115

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
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1363062; hg19: chr2-54281762;