Variant 13-94574874-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000261296.7(TGDS):c.983-23_983-22insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0515 in 928,724 control chromosomes in the GnomAD database, including 53 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.024 ( 41 hom., cov: 30)

Exomes 𝑓: 0.055 ( 12 hom. )

Consequence

TGDS
ENST00000261296.7 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.60

Variant links:

Genes affected

TGDS (HGNC:20324): (TDP-glucose 4,6-dehydratase) The protein encoded by this gene is a member of the short-chain dehydrogenases/reductases (SDR) superfamily, and is thought to contain a nicotinamide adenine dinucleotide (NAD) binding domain. This large SDR family of enzymes is involved in the metabolism of a variety of compounds, including prostaglandins, retinoids, lipids, steroid hormones, and xenobiotics. Mutations in this gene have been associated with Catel-Manzke syndrome, which is characterized by Pierre Robin sequence, and radial deviation of the index finger due to the presence of an accessory bone between the index finger and its proximal phalanx. Pierre Robin sequence is defined by an undersized jaw, backwards displacement of the tongue base that causes an obstruction of the airways, and can also be associated with a cleft palate. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

TGDS links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 13-94574874-C-CA is Benign according to our data. Variant chr13-94574874-C-CA is described in ClinVar as [Benign]. Clinvar id is 1261515.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TGDS	NM_014305.4 linkuse as main transcript	c.983-23_983-22insT		intron_variant		ENST00000261296.7	NP_055120.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TGDS	ENST00000261296.7 linkuse as main transcript	c.983-23_983-22insT		intron_variant		1	NM_014305.4	ENSP00000261296	P1

Frequencies

GnomAD3 genomes

AF:

0.0244

AC:

2568

AN:

105244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0713

Gnomad AMI

AF:

0.0289

Gnomad AMR

AF:

0.0118

Gnomad ASJ

AF:

0.0232

Gnomad EAS

AF:

0.00398

Gnomad SAS

AF:

0.00770

Gnomad FIN

AF:

0.00438

Gnomad MID

AF:

0.0385

Gnomad NFE

AF:

0.0129

Gnomad OTH

AF:

0.0233

GnomAD3 exomes

AF:

0.0926

AC:

4970

AN:

53648

Hom.:

AF XY:

0.0906

AC XY:

2629

AN XY:

29028

show subpopulations

Gnomad AFR exome

AF:

0.180

Gnomad AMR exome

AF:

0.109

Gnomad ASJ exome

AF:

0.0989

Gnomad EAS exome

AF:

0.106

Gnomad SAS exome

AF:

0.0803

Gnomad FIN exome

AF:

0.0641

Gnomad NFE exome

AF:

0.0820

Gnomad OTH exome

AF:

0.0912

GnomAD4 exome

AF:

0.0550

AC:

45278

AN:

823458

Hom.:

Cov.:

AF XY:

0.0553

AC XY:

22840

AN XY:

412856

show subpopulations

Gnomad4 AFR exome

AF:

0.0619

Gnomad4 AMR exome

AF:

0.0652

Gnomad4 ASJ exome

AF:

0.0694

Gnomad4 EAS exome

AF:

0.0662

Gnomad4 SAS exome

AF:

0.0640

Gnomad4 FIN exome

AF:

0.0443

Gnomad4 NFE exome

AF:

0.0533

Gnomad4 OTH exome

AF:

0.0576

GnomAD4 genome

AF:

0.0245

AC:

2577

AN:

105266

Hom.:

Cov.:

AF XY:

0.0236

AC XY:

1201

AN XY:

50786

show subpopulations

Gnomad4 AFR

AF:

0.0714

Gnomad4 AMR

AF:

0.0119

Gnomad4 ASJ

AF:

0.0232

Gnomad4 EAS

AF:

0.00400

Gnomad4 SAS

AF:

0.00801

Gnomad4 FIN

AF:

0.00438

Gnomad4 NFE

AF:

0.0129

Gnomad4 OTH

AF:

0.0232

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over