2-53993761-G-A

Variant names:

• chr2-53993761-G-A
• rs6545379
• NM_001320586.2:c.62+19951G>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.62+19951G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,070 control chromosomes in the GnomAD database, including 45,388 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 0.76 (45388 hom., cov: 31)
• Consequence: ACYP2 NM_001320586.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 9 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001320586.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACYP2	NM_001320586.2		c.62+19951G>A		intron	N/A	NP_001307515.1
	ACYP2	NM_001320587.2		c.62+19951G>A		intron	N/A	NP_001307516.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACYP2	ENST00000607452.6	TSL:2	c.62+19951G>A		intron	N/A	ENSP00000475986.1
	ACYP2	ENST00000422521.2	TSL:5	c.62+19951G>A		intron	N/A	ENSP00000475658.1
	ACYP2	ENST00000458030.3	TSL:3	n.582+19951G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115919 AN: 151954 Hom.: 45341 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.763 AC: 116023 AN: 152070 Hom.: 45388 Cov.: 31 AF XY: 0.768 AC XY: 57082 AN XY: 74336

African (AFR) AF: 0.936 AC: 38860 AN: 41506

American (AMR) AF: 0.703 AC: 10727 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2189 AN: 3466

East Asian (EAS) AF: 0.924 AC: 4784 AN: 5180

South Asian (SAS) AF: 0.779 AC: 3746 AN: 4808

European-Finnish (FIN) AF: 0.753 AC: 7952 AN: 10562

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45325 AN: 67964

Other (OTH) AF: 0.746 AC: 1575 AN: 2110

Alfa AF: 0.694 Hom.: 47270

Bravo AF: 0.769

Asia WGS AF: 0.857 AC: 2983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		0.12
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: rs6545379; hg19: chr2-54220898;