rs7303

Variant names:

• chr14-75053362-T-C
• rs7303
• NM_001107.5:c.*82A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001107.5(ACYP1):​c.*82A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 1,253,614 control chromosomes in the GnomAD database, including 155,487 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 0.43 (15995 hom., cov: 32)
  • Exomes 𝑓: 0.49 (139492 hom.)
• Consequence: ACYP1 NM_001107.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 33 publications found

Genes affected

ACYP1 (HGNC:179): (acylphosphatase 1) This gene is a member of the acylphosphatase family. The encoded protein is a small cytosolic enzyme that catalyzes the hydrolysis of the carboxyl-phosphate bond of acylphosphates. Two isoenzymes have been isolated and described based on their tissue localization: erythrocyte (common) type acylphosphatase encoded by this gene, and muscle type acylphosphatase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001107.5. 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
	ACYP1	NM_001107.5	MANE Select	c.*82A>G		3_prime_UTR	Exon 3 of 3	NP_001098.1
	ACYP1	NR_126393.2		n.540A>G		non_coding_transcript_exon	Exon 4 of 4
	ACYP1	NR_126394.2		n.579A>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACYP1	ENST00000238618.8	TSL:1 MANE Select	c.*82A>G		3_prime_UTR	Exon 3 of 3	ENSP00000238618.3
	ACYP1	ENST00000555463.1	TSL:2	c.*82A>G		3_prime_UTR	Exon 3 of 3	ENSP00000450873.1
	ACYP1	ENST00000555694.5	TSL:3	c.*82A>G		3_prime_UTR	Exon 3 of 3	ENSP00000451581.1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65932 AN: 151962 Hom.: 15986 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.449

GnomAD4 exome AF: 0.494 AC: 543947 AN: 1101534 Hom.: 139492 Cov.: 15 AF XY: 0.492 AC XY: 275890 AN XY: 560996

African (AFR) AF: 0.224 AC: 5766 AN: 25730

American (AMR) AF: 0.708 AC: 28954 AN: 40886

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 10227 AN: 22390

East Asian (EAS) AF: 0.828 AC: 31442 AN: 37978

South Asian (SAS) AF: 0.448 AC: 33053 AN: 73754

European-Finnish (FIN) AF: 0.477 AC: 23774 AN: 49824

Middle Eastern (MID) AF: 0.436 AC: 1588 AN: 3642

European-Non Finnish (NFE) AF: 0.483 AC: 385661 AN: 799112

Other (OTH) AF: 0.487 AC: 23482 AN: 48218

GnomAD4 genome AF: 0.434 AC: 65963 AN: 152080 Hom.: 15995 Cov.: 32 AF XY: 0.438 AC XY: 32595 AN XY: 74342

African (AFR) AF: 0.230 AC: 9542 AN: 41484

American (AMR) AF: 0.587 AC: 8967 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3468

East Asian (EAS) AF: 0.835 AC: 4325 AN: 5178

South Asian (SAS) AF: 0.443 AC: 2133 AN: 4818

European-Finnish (FIN) AF: 0.487 AC: 5137 AN: 10554

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32808 AN: 67982

Other (OTH) AF: 0.444 AC: 936 AN: 2110

Alfa AF: 0.465 Hom.: 39452

Bravo AF: 0.437

Asia WGS AF: 0.572 AC: 1987 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	12
DANN	Benign	0.87
PhyloP100		0.33
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7303; hg19: chr14-75520065;