Genetic Variant AADAC: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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488869.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
AADACL2-AS1	NR_110202.1		n.320-39441G>A	intron	N/A
AADACL2-AS1	NR_110203.1		n.320-39441G>A	intron	N/A
AADAC	NM_001086.3	MANE Select	c.-57C>T	upstream_gene	N/A	NP_001077.2	P22760

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
AADAC	ENST00000854459.1	c.-57C>T	5_prime_UTR	Exon 1 of 6	ENSP00000524518.1
AADAC	ENST00000854460.1	c.-57C>T	5_prime_UTR	Exon 1 of 5	ENSP00000524519.1
AADAC	ENST00000854456.1	c.-57C>T	5_prime_UTR	Exon 1 of 5	ENSP00000524515.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over