dbSNP rs9990: 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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADO	NM_032804.6 link	c.*2306C>T		3_prime_UTR_variant	Exon 1 of 1	ENST00000373783.3	NP_116193.2	Q96SZ5B3KXN9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADO	ENST00000373783.3 link	c.*2306C>T		3_prime_UTR_variant	Exon 1 of 1	6	NM_032804.6	ENSP00000362888.1		Q96SZ5
ADO	ENST00000710287.1 link	c.*2306C>T		3_prime_UTR_variant	Exon 1 of 1			ENSP00000518177.1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over