rs9990

chr10-62808178-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ADO	NM_032804.6	c.*2306C>T		3_prime_UTR_variant	1/1	ENST00000373783.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADO	ENST00000373783.3	c.*2306C>T		3_prime_UTR_variant	1/1		NM_032804.6	P1
ADO	ENST00000710287.1	c.*2306C>T		3_prime_UTR_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34914 AN: 151924 Hom.: 5009 Cov.: 33

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.: 0 AF XY: 0.227 AC XY: 1623 AN XY: 7140

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.130

Gnomad4 FIN exome AF: 0.224

Gnomad4 NFE exome AF: 0.131

Gnomad4 OTH exome AF: 0.244

GnomAD4 genome AF: 0.230 AC: 35002 AN: 152042 Hom.: 5032 Cov.: 33 AF XY: 0.234 AC XY: 17418 AN XY: 74320

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.212

Alfa AF: 0.157 Hom.: 2567

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	13
Dann	Benign	0.80

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

LitVar

Other links and lift over

dbSNP: rs9990; hg19: chr10-64567938; COSMIC: COSV54348957; COSMIC: COSV54348957;