rs1862121

Variant names:

• chr2-54058102-G-A
• rs1862121
• NM_001320586.2:c.277+742G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-54058102-G-A
• chr2-54058102-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 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.277+742G>A		intron	N/A	NP_001307515.1
	ACYP2	NM_001320587.2		c.184+742G>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.277+742G>A		intron	N/A	ENSP00000475986.1
	ACYP2	ENST00000422521.2	TSL:5	c.277+742G>A		intron	N/A	ENSP00000475658.1
	ACYP2	ENST00000458030.3	TSL:3	n.797+742G>A		intron	N/A

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

African (AFR) AF: 0.279 AC: 11530 AN: 41392

American (AMR) AF: 0.364 AC: 5547 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3470

East Asian (EAS) AF: 0.716 AC: 3697 AN: 5166

South Asian (SAS) AF: 0.556 AC: 2678 AN: 4814

European-Finnish (FIN) AF: 0.521 AC: 5483 AN: 10524

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25889 AN: 67912

Other (OTH) AF: 0.378 AC: 796 AN: 2104

Alfa AF: 0.373 Hom.: 40730

Bravo AF: 0.362

Asia WGS AF: 0.643 AC: 2228 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.1
DANN	Benign	0.57
PhyloP100		-0.43
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: rs1862121; hg19: chr2-54285239;