rs843748

chr2-54275775-G-A

Variant summary

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

The NM_001320586.2(ACYP2):c.405-28913G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,988 control chromosomes in the GnomAD database, including 11,827 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 0.36 (11827 hom., cov: 32)
• Consequence: ACYP2 NM_001320586.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACYP2	NM_001320586.2	c.405-28913G>A		intron_variant		ENST00000607452.6
LOC105374610	XR_007086321.1	n.1295+2569C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACYP2	ENST00000607452.6	c.405-28913G>A		intron_variant		2	NM_001320586.2

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55404 AN: 151870 Hom.: 11825 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.365 AC: 55405 AN: 151988 Hom.: 11827 Cov.: 32 AF XY: 0.365 AC XY: 27079 AN XY: 74282

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.344

Alfa AF: 0.439 Hom.: 31736

Bravo AF: 0.347

Asia WGS AF: 0.243 AC: 844 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.3
Dann	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs843748; hg19: chr2-54502912;