Genetic Variant ENST00000488869.1:c.-57C>T (chr3-151814106-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 ENST00000488869.1(AADAC):c.-57C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,589,212 control chromosomes in the GnomAD database, including 80,337 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 0.31 ( 7490 hom., cov: 31)

Exomes 𝑓: 0.31 ( 72847 hom. )

Consequence

AADAC
ENST00000488869.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.654

Publications

11 publications found

Variant links:

Genes affected

AADAC (HGNC:17): (arylacetamide deacetylase) Microsomal arylacetamide deacetylase competes against the activity of cytosolic arylamine N-acetyltransferase, which catalyzes one of the initial biotransformation pathways for arylamine and heterocyclic amine carcinogens [provided by RefSeq, Jul 2008]

AADAC links:

AADACL2-AS1 (HGNC:50301): (AADACL2 antisense RNA 1)

AADACL2-AS1 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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
AADACL2-AS1	NR_110202.1 link	n.320-39441G>A	intron_variant	Intron 1 of 3
AADACL2-AS1	NR_110203.1 link	n.320-39441G>A	intron_variant	Intron 1 of 2
AADAC	NM_001086.3 link	c.-57C>T	upstream_gene_variant		ENST00000232892.12	NP_001077.2	P22760
AADAC	XM_005247104.5 link	c.-57C>T	upstream_gene_variant			XP_005247161.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AADAC	ENST00000232892.12 link	c.-57C>T		upstream_gene_variant		1	NM_001086.3	ENSP00000232892.6		P22760

Frequencies

GnomAD3 genomes

AF:

0.305

AC:

46281

AN:

151540

Hom.:

7482

Cov.:

show subpopulations

Gnomad AFR

AF:

0.293

Gnomad AMI

AF:

0.334

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.326

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.205

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.324

Gnomad OTH

AF:

0.310

GnomAD4 exome

AF:

0.312

AC:

447979

AN:

1437554

Hom.:

72847

Cov.:

AF XY:

0.310

AC XY:

222439

AN XY:

716612

show subpopulations

African (AFR)

AF:

0.292

AC:

9654

AN:

33036

American (AMR)

AF:

0.383

AC:

17009

AN:

44420

Ashkenazi Jewish (ASJ)

AF:

0.280

AC:

7261

AN:

25960

East Asian (EAS)

AF:

0.315

AC:

12464

AN:

39558

South Asian (SAS)

AF:

0.259

AC:

22192

AN:

85750

European-Finnish (FIN)

AF:

0.218

AC:

11565

AN:

53162

Middle Eastern (MID)

AF:

0.334

AC:

1919

AN:

5744

European-Non Finnish (NFE)

AF:

0.319

AC:

347564

AN:

1090360

Other (OTH)

AF:

0.308

AC:

18351

AN:

59564

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

15083

30165

45248

60330

75413

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11120

22240

33360

44480

55600

<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:

0.305

AC:

46314

AN:

151658

Hom.:

7490

Cov.:

AF XY:

0.299

AC XY:

22154

AN XY:

74062

show subpopulations

African (AFR)

AF:

0.293

AC:

12112

AN:

41388

American (AMR)

AF:

0.338

AC:

5153

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

981

AN:

3470

East Asian (EAS)

AF:

0.327

AC:

1687

AN:

5162

South Asian (SAS)

AF:

0.253

AC:

1217

AN:

4804

European-Finnish (FIN)

AF:

0.205

AC:

2142

AN:

10456

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.324

AC:

21980

AN:

67854

Other (OTH)

AF:

0.310

AC:

652

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1612

3224

4835

6447

8059

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

454

908

1362

1816

2270

<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:

0.317

Hom.:

23988

Bravo

AF:

0.316

Asia WGS

AF:

0.284

AC:

986

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.5

(source)

DANN

Benign

0.75

PhyloP100

0.65

PromoterAI

-0.16

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

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