rs1862121

chr2-54058102-G-Achr2-54058102-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001320586.2(ACYP2):c.277+742G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,828 control chromosomes in the GnomAD database, including 11,617 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 0.38 (11617 hom., cov: 31)
• Consequence: ACYP2 NM_001320586.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACYP2	NM_001320586.2	c.277+742G>A		intron_variant		ENST00000607452.6
ACYP2	NM_001320587.2	c.184+742G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACYP2	ENST00000607452.6	c.277+742G>A		intron_variant		2	NM_001320586.2
ACYP2	ENST00000422521.2	c.277+742G>A		intron_variant		5
ACYP2	ENST00000458030.3	n.797+742G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57410 AN: 151710 Hom.: 11615 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.378 AC: 57432 AN: 151828 Hom.: 11617 Cov.: 31 AF XY: 0.389 AC XY: 28845 AN XY: 74180

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.378

Alfa AF: 0.370 Hom.: 17044

Bravo AF: 0.362

Asia WGS AF: 0.643 AC: 2228 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	8.1
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1862121; hg19: chr2-54285239;