rs7303

Positions:

• chr14-75053362-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000238618.8(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 ENST00000238618.8 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACYP1	NM_001107.5	c.*82A>G		3_prime_UTR_variant	3/3	ENST00000238618.8	NP_001098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACYP1	ENST00000238618.8	c.*82A>G		3_prime_UTR_variant	3/3	1	NM_001107.5	ENSP00000238618	P1
ACYP1	ENST00000357971.7	c.*293A>G		3_prime_UTR_variant	4/4	3		ENSP00000350655
ACYP1	ENST00000555463.1	c.*82A>G		3_prime_UTR_variant	3/3	2		ENSP00000450873
ACYP1	ENST00000555694.5	c.*82A>G		3_prime_UTR_variant	3/3	3		ENSP00000451581	P1

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

Gnomad4 AFR exome AF: 0.224

Gnomad4 AMR exome AF: 0.708

Gnomad4 ASJ exome AF: 0.457

Gnomad4 EAS exome AF: 0.828

Gnomad4 SAS exome AF: 0.448

Gnomad4 FIN exome AF: 0.477

Gnomad4 NFE exome AF: 0.483

Gnomad4 OTH exome AF: 0.487

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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.444

Alfa AF: 0.484 Hom.: 23013

Bravo AF: 0.437

Asia WGS AF: 0.572 AC: 1987 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	12
DANN	Benign	0.87
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs7303; hg19: chr14-75520065;