rs1974771

Variant names:

• chr2-54051406-G-A
• rs1974771
• NM_001320586.2:c.155+356G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-54051406-G-A
• chr2-54051406-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.155+356G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 727,612 control chromosomes in the GnomAD database, including 5,027 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 0.096 (795 hom., cov: 32)
  • Exomes 𝑓: 0.11 (4232 hom.)
• Consequence: ACYP2 NM_001320586.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.46
• Publications: 4 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]

HMGB1P31 (HGNC:39122): (high mobility group box 1 pseudogene 31)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACYP2	NM_001320586.2		c.155+356G>A		intron	N/A	NP_001307515.1	U3KQL2
	ACYP2	NM_001320587.2		c.63-5833G>A		intron	N/A	NP_001307516.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACYP2	ENST00000607452.6	TSL:2	c.155+356G>A		intron	N/A	ENSP00000475986.1	U3KQL2
	ACYP2	ENST00000422521.2	TSL:5	c.155+356G>A		intron	N/A	ENSP00000475658.1	U3KQ94
	HMGB1P31	ENST00000437242.1	TSL:6	n.73G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14590 AN: 152034 Hom.: 792 Cov.: 32

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.115 AC: 65942 AN: 575460 Hom.: 4232 Cov.: 0 AF XY: 0.112 AC XY: 35378 AN XY: 314578

African (AFR) AF: 0.0452 AC: 706 AN: 15622

American (AMR) AF: 0.156 AC: 5569 AN: 35628

Ashkenazi Jewish (ASJ) AF: 0.0950 AC: 1784 AN: 18776

East Asian (EAS) AF: 0.221 AC: 7853 AN: 35528

South Asian (SAS) AF: 0.0788 AC: 5011 AN: 63622

European-Finnish (FIN) AF: 0.164 AC: 6889 AN: 42104

Middle Eastern (MID) AF: 0.0982 AC: 225 AN: 2292

European-Non Finnish (NFE) AF: 0.105 AC: 34673 AN: 331358

Other (OTH) AF: 0.106 AC: 3232 AN: 30530

GnomAD4 genome AF: 0.0960 AC: 14607 AN: 152152 Hom.: 795 Cov.: 32 AF XY: 0.0986 AC XY: 7335 AN XY: 74368

African (AFR) AF: 0.0442 AC: 1835 AN: 41512

American (AMR) AF: 0.104 AC: 1585 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3466

East Asian (EAS) AF: 0.240 AC: 1244 AN: 5176

South Asian (SAS) AF: 0.0863 AC: 416 AN: 4822

European-Finnish (FIN) AF: 0.167 AC: 1772 AN: 10580

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7059 AN: 67992

Other (OTH) AF: 0.113 AC: 239 AN: 2108

Alfa AF: 0.0654 Hom.: 112

Bravo AF: 0.0929

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		2.5
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1974771; hg19: chr2-54278543; COSMIC: COSV69707046;