rs6545379

chr2-53993761-G-Achr2-53993761-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACYP2	NM_001320586.2	c.62+19951G>A		intron_variant		ENST00000607452.6
ACYP2	NM_001320587.2	c.62+19951G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACYP2	ENST00000607452.6	c.62+19951G>A		intron_variant		2	NM_001320586.2
ACYP2	ENST00000422521.2	c.62+19951G>A		intron_variant		5
ACYP2	ENST00000458030.3	n.582+19951G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.746

Alfa AF: 0.682 Hom.: 34562

Bravo AF: 0.769

Asia WGS AF: 0.857 AC: 2983 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	1.8
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6545379; hg19: chr2-54220898;