NM_001320586.2:c.405-55959C>A

Variant names:

• chr2-54248729-C-A
• rs11125529
• NM_001320586.2:c.405-55959C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001320586.2(ACYP2):​c.405-55959C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,126 control chromosomes in the GnomAD database, including 1,611 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.15 (1611 hom., cov: 32)
• Consequence: ACYP2 NM_001320586.2 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -1.38
• Publications: 95 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]

LOC105374610 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACYP2	NM_001320586.2	c.405-55959C>A		intron_variant	Intron 6 of 6	ENST00000607452.6	NP_001307515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACYP2	ENST00000607452.6	c.405-55959C>A		intron_variant	Intron 6 of 6	2	NM_001320586.2	ENSP00000475986.1
ACYP2	ENST00000394666.9	c.186-55959C>A		intron_variant	Intron 3 of 3	1		ENSP00000378161.3

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22061 AN: 152008 Hom.: 1610 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.145 AC: 22076 AN: 152126 Hom.: 1611 Cov.: 32 AF XY: 0.145 AC XY: 10769 AN XY: 74380

African (AFR) AF: 0.182 AC: 7555 AN: 41496

American (AMR) AF: 0.116 AC: 1774 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3468

East Asian (EAS) AF: 0.160 AC: 829 AN: 5180

South Asian (SAS) AF: 0.100 AC: 485 AN: 4826

European-Finnish (FIN) AF: 0.123 AC: 1306 AN: 10576

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.137 AC: 9339 AN: 67980

Other (OTH) AF: 0.119 AC: 251 AN: 2114

Alfa AF: 0.132 Hom.: 1975

Bravo AF: 0.147

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Chronic osteomyelitis Other:1

Sep 01, 2016

Department of Orthopeadics and Traumatology, Nanfang Hospital

Significance: association

Review Status: no assertion criteria provided

Collection Method: case-control

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.68
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11125529; hg19: chr2-54475866;