Genetic Variant ADO:c.*2306C>T (chr10-62808178-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_032804.6(ADO):c.*2306C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 167,054 control chromosomes in the GnomAD database, including 5,438 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 0.23 ( 5032 hom., cov: 33)

Exomes 𝑓: 0.22 ( 406 hom. )

Consequence

ADO
NM_032804.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0200

Publications

11 publications found

Variant links:

Genes affected

ADO (HGNC:23506): (2-aminoethanethiol dioxygenase) Human thiol dioxygenases include cysteine dioxygenase (CDO; MIM 603943) and cysteamine (2-aminoethanethiol) dioxygenase (ADO; EC 1.13.11.19). CDO adds 2 oxygen atoms to free cysteine, whereas ADO adds 2 oxygen atoms to free cysteamine to form hypotaurine (Dominy et al., 2007 [PubMed 17581819]).[supplied by OMIM, Mar 2008]

ADO links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032804.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADO	NM_032804.6	MANE Select	c.*2306C>T		3_prime_UTR	Exon 1 of 1	NP_116193.2	Q96SZ5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADO	ENST00000373783.3	TSL:6 MANE Select	c.*2306C>T		3_prime_UTR	Exon 1 of 1	ENSP00000362888.1	Q96SZ5
	ADO	ENST00000710287.1		c.*2306C>T		3_prime_UTR	Exon 1 of 1	ENSP00000518177.1	A0AA34QVG9

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

34914

AN:

151924

Hom.:

5009

Cov.:

show subpopulations

Gnomad AFR

AF:

0.361

Gnomad AMI

AF:

0.187

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.0718

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.240

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.208

GnomAD4 exome

AF:

0.223

AC:

3346

AN:

15012

Hom.:

406

Cov.:

AF XY:

0.227

AC XY:

1623

AN XY:

7140

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.130

AC:

AN:

138

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.224

AC:

3291

AN:

14690

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.131

AC:

AN:

Other (OTH)

AF:

0.244

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

142

284

425

567

709

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.230

AC:

35002

AN:

152042

Hom.:

5032

Cov.:

AF XY:

0.234

AC XY:

17418

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.362

AC:

14988

AN:

41452

American (AMR)

AF:

0.311

AC:

4753

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0718

AC:

249

AN:

3468

East Asian (EAS)

AF:

0.435

AC:

2249

AN:

5174

South Asian (SAS)

AF:

0.241

AC:

1161

AN:

4822

European-Finnish (FIN)

AF:

0.213

AC:

2249

AN:

10554

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.128

AC:

8685

AN:

67984

Other (OTH)

AF:

0.212

AC:

448

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1288

2576

3864

5152

6440

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.167

Hom.:

3766

Bravo

AF:

0.247

Asia WGS

AF:

0.360

AC:

1248

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.24

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

0.020

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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