Variant 2-54057304-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001320586.2(ACYP2):c.221G>A(p.Trp74*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0974 in 397,870 control chromosomes in the GnomAD database, including 2,258 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.091 ( 818 hom., cov: 33)

Exomes 𝑓: 0.10 ( 1440 hom. )

Consequence

ACYP2
NM_001320586.2 stop_gained

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.958

Variant links:

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]

ACYP2 links:

ACYP2 (HGNC:):

ACYP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-54057304-G-A is Benign according to our data. Variant chr2-54057304-G-A is described in ClinVar as [Benign]. Clinvar id is 2799781.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACYP2	NM_001320586.2 linkuse as main transcript	c.221G>A	p.Trp74*	stop_gained	4/7	ENST00000607452.6	NP_001307515.1	U3KQL2
ACYP2	NM_001320587.2 linkuse as main transcript	c.128G>A	p.Trp43*	stop_gained	3/6		NP_001307516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ACYP2	ENST00000607452.6 linkuse as main transcript	c.221G>A	p.Trp74*	stop_gained	4/7	2	NM_001320586.2	ENSP00000475986.1	U3KQL2
ACYP2	ENST00000422521.2 linkuse as main transcript	c.221G>A	p.Trp74*	stop_gained	4/5	5		ENSP00000475658.1	U3KQ94
ACYP2	ENST00000458030.3 linkuse as main transcript	n.741G>A		non_coding_transcript_exon_variant	4/5	3

Frequencies

GnomAD3 genomes

AF:

0.0911

AC:

13848

AN:

152060

Hom.:

814

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0258

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.0267

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.0831

GnomAD4 exome

AF:

0.101

AC:

24900

AN:

245692

Hom.:

1440

Cov.:

AF XY:

0.102

AC XY:

12758

AN XY:

124524

show subpopulations

Gnomad4 AFR exome

AF:

0.0269

Gnomad4 AMR exome

AF:

0.126

Gnomad4 ASJ exome

AF:

0.114

Gnomad4 EAS exome

AF:

0.0123

Gnomad4 SAS exome

AF:

0.194

Gnomad4 FIN exome

AF:

0.145

Gnomad4 NFE exome

AF:

0.108

Gnomad4 OTH exome

AF:

0.100

GnomAD4 genome

AF:

0.0911

AC:

13858

AN:

152178

Hom.:

818

Cov.:

AF XY:

0.0958

AC XY:

7124

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0258

Gnomad4 AMR

AF:

0.121

Gnomad4 ASJ

AF:

0.114

Gnomad4 EAS

AF:

0.0266

Gnomad4 SAS

AF:

0.190

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.112

Gnomad4 OTH

AF:

0.0836

Alfa

AF:

0.107

Hom.:

1079

Bravo

AF:

0.0856

TwinsUK

AF:

0.112

AC:

417

ALSPAC

AF:

0.117

AC:

451

ExAC

AF:

0.0218

AC:

Asia WGS

AF:

0.115

AC:

399

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 17, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.25

BayesDel_noAF

Uncertain

-0.010

CADD

Pathogenic

DANN

Benign

0.47

FATHMM_MKL

Benign

0.013

Vest4

0.060

GERP RS

0.96

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over