Variant 13-94574884-AAAG-A 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.983-35_983-33del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 1,260,708 control chromosomes in the GnomAD database, including 13,249 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.29 ( 7320 hom., cov: 0)

Exomes 𝑓: 0.18 ( 5929 hom. )

Consequence

TGDS
ENST00000261296.7 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.389

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 13-94574884-AAAG-A is Benign according to our data. Variant chr13-94574884-AAAG-A is described in ClinVar as [Benign]. Clinvar id is 1282312.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 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.983-35_983-33del		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.983-35_983-33del		intron_variant		1	NM_014305.4	ENSP00000261296	P1

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

43737

AN:

148384

Hom.:

7320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.477

Gnomad AMI

AF:

0.194

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.00404

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.261

Gnomad OTH

AF:

0.273

GnomAD3 exomes

AF:

0.111

AC:

16910

AN:

151682

Hom.:

818

AF XY:

0.107

AC XY:

8830

AN XY:

82302

show subpopulations

Gnomad AFR exome

AF:

0.338

Gnomad AMR exome

AF:

0.0653

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.00177

Gnomad SAS exome

AF:

0.0670

Gnomad FIN exome

AF:

0.0881

Gnomad NFE exome

AF:

0.137

Gnomad OTH exome

AF:

0.127

GnomAD4 exome

AF:

0.182

AC:

202480

AN:

1112224

Hom.:

5929

AF XY:

0.180

AC XY:

100706

AN XY:

560830

show subpopulations

Gnomad4 AFR exome

AF:

0.365

Gnomad4 AMR exome

AF:

0.0840

Gnomad4 ASJ exome

AF:

0.169

Gnomad4 EAS exome

AF:

0.00153

Gnomad4 SAS exome

AF:

0.116

Gnomad4 FIN exome

AF:

0.168

Gnomad4 NFE exome

AF:

0.195

Gnomad4 OTH exome

AF:

0.185

GnomAD4 genome

AF:

0.295

AC:

43752

AN:

148484

Hom.:

7320

Cov.:

AF XY:

0.285

AC XY:

20678

AN XY:

72452

show subpopulations

Gnomad4 AFR

AF:

0.476

Gnomad4 AMR

AF:

0.187

Gnomad4 ASJ

AF:

0.238

Gnomad4 EAS

AF:

0.00405

Gnomad4 SAS

AF:

0.159

Gnomad4 FIN

AF:

0.210

Gnomad4 NFE

AF:

0.261

Gnomad4 OTH

AF:

0.273

Alfa

AF:

0.269

Hom.:

413

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 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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