Genetic Variant ACY3:c.-88G>A (chr11-67647583-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.374

Publications

14 publications found

Variant links:

Genes affected

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

ACY3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ACY3	NM_080658.2 link	c.-88G>A		5_prime_UTR_variant	Exon 2 of 8	ENST00000255082.8	NP_542389.1	Q96HD9A0A024R5L2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACY3	ENST00000255082.8 link	c.-88G>A		5_prime_UTR_variant	Exon 2 of 8	1	NM_080658.2	ENSP00000255082.3		Q96HD9
ACY3	ENST00000529256.1 link	c.-313G>A		5_prime_UTR_variant	Exon 1 of 7	3		ENSP00000434270.1		E9PRA7

Frequencies

GnomAD3 genomes

AF:

0.802

AC:

121146

AN:

151060

Hom.:

48884

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.727

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.900

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.842

AC:

AN:

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.802

AC:

121229

AN:

151180

Hom.:

48911

Cov.:

AF XY:

0.807

AC XY:

59600

AN XY:

73824

show subpopulations

African (AFR)

AF:

0.707

AC:

29031

AN:

41038

American (AMR)

AF:

0.837

AC:

12736

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.866

AC:

3006

AN:

3472

East Asian (EAS)

AF:

0.767

AC:

3868

AN:

5042

South Asian (SAS)

AF:

0.923

AC:

4427

AN:

4796

European-Finnish (FIN)

AF:

0.906

AC:

9501

AN:

10482

Middle Eastern (MID)

AF:

0.816

AC:

240

AN:

294

European-Non Finnish (NFE)

AF:

0.826

AC:

56065

AN:

67840

Other (OTH)

AF:

0.792

AC:

1659

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1207

2413

3620

4826

6033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

868

1736

2604

3472

4340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.812

Hom.:

76314

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

(source)

DANN

Benign

0.66

PhyloP100

0.37

PromoterAI

0.17

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over