chr5-115813260-T-TA

Position:

• chr5-115813260-T-TA

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6

The NM_001801.3(CDO1):​c.171-3dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00196 in 1,494,548 control chromosomes in the GnomAD database, including 2 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.00039 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0021 (1 hom.)
• Consequence: CDO1 NM_001801.3 splice_region, intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 2.43

Genes affected

CDO1 (HGNC:1795): (cysteine dioxygenase type 1) Predicted to enable cysteine dioxygenase activity and ferrous iron binding activity. Predicted to be involved in L-cysteine catabolic process. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

CDO1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BP6: Variant 5-115813260-T-TA is Benign according to our data. Variant chr5-115813260-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 3037994.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDO1	NM_001801.3	c.171-3dupT		splice_region_variant, intron_variant		ENST00000250535.5	NP_001792.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDO1	ENST00000250535.5	c.171-3dupT		splice_region_variant, intron_variant		1	NM_001801.3	ENSP00000250535.4
CDO1	ENST00000502631.1	n.75-3dupT		splice_region_variant, intron_variant		3
CDO1	ENST00000504613.1	n.488-3dupT		splice_region_variant, intron_variant		4
CDO1	ENST00000504877.1	n.197-3dupT		splice_region_variant, intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.000386 AC: 58 AN: 150246 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000686

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000133

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.000582

Gnomad SAS AF: 0.000840

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000237

Gnomad OTH AF: 0.000488

GnomAD4 exome AF: 0.00214 AC: 2874 AN: 1344194 Hom.: 1 Cov.: 22 AF XY: 0.00202 AC XY: 1360 AN XY: 673530

Gnomad4 AFR exome AF: 0.00221

Gnomad4 AMR exome AF: 0.00188

Gnomad4 ASJ exome AF: 0.00286

Gnomad4 EAS exome AF: 0.000759

Gnomad4 SAS exome AF: 0.00160

Gnomad4 FIN exome AF: 0.000134

Gnomad4 NFE exome AF: 0.00232

Gnomad4 OTH exome AF: 0.00223

GnomAD4 genome AF: 0.000386 AC: 58 AN: 150354 Hom.: 1 Cov.: 32 AF XY: 0.000340 AC XY: 25 AN XY: 73432

Gnomad4 AFR AF: 0.000684

Gnomad4 AMR AF: 0.000133

Gnomad4 ASJ AF: 0.00116

Gnomad4 EAS AF: 0.000583

Gnomad4 SAS AF: 0.000841

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000237

Gnomad4 OTH AF: 0.000483

Asia WGS AF: 0.00173 AC: 6 AN: 3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

CDO1-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 19, 2021

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

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: rs571899483; hg19: chr5-115148957;