11-67647583-C-T

Position:

• chr11-67647583-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080658.2(ACY3):​c.-88G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 151,244 control chromosomes in the GnomAD database, including 48,932 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 0.80 (48911 hom., cov: 26)
  • Exomes 𝑓: 0.80 (21 hom.)
• Consequence: ACY3 NM_080658.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

Genes affected

ACY3 (HGNC:24104): (aminoacylase 3) Predicted to enable aminoacylase activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACY3	NM_080658.2	c.-88G>A		5_prime_UTR_variant	2/8	ENST00000255082.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACY3	ENST00000255082.8	c.-88G>A		5_prime_UTR_variant	2/8	1	NM_080658.2	P1
ACY3	ENST00000529256.1	c.-313G>A		5_prime_UTR_variant	1/7	3

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121146 AN: 151060 Hom.: 48884 Cov.: 26

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.790

GnomAD4 exome AF: 0.797 AC: 51 AN: 64 Hom.: 21 Cov.: 0 AF XY: 0.727 AC XY: 32 AN XY: 44

Gnomad4 AFR exome AF: 0.250

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.900

Gnomad4 NFE exome AF: 0.842

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.802 AC: 121229 AN: 151180 Hom.: 48911 Cov.: 26 AF XY: 0.807 AC XY: 59600 AN XY: 73824

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.792

Alfa AF: 0.816 Hom.: 44800

Bravo AF: 0.791

Asia WGS AF: 0.816 AC: 2832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.6
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs2514036; hg19: chr11-67415054; COSMIC: COSV54828054; COSMIC: COSV54828054;