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

Variant summary

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

The NM_014305.4(TGDS):c.983-23del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0889 in 874,594 control chromosomes in the GnomAD database, including 10 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 1 hom., cov: 30)

Exomes 𝑓: 0.10 ( 9 hom. )

Consequence

TGDS
NM_014305.4 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-CA-C is Benign according to our data. Variant chr13-94574874-CA-C is described in ClinVar as [Benign]. Clinvar id is 1244089.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TGDS	NM_014305.4 linkuse as main transcript	c.983-23del		intron_variant		ENST00000261296.7

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.00442

AC:

465

AN:

105096

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00119

Gnomad AMI

AF:

0.00826

Gnomad AMR

AF:

0.00588

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00133

Gnomad SAS

AF:

0.00239

Gnomad FIN

AF:

0.00848

Gnomad MID

AF:

0.00855

Gnomad NFE

AF:

0.00562

Gnomad OTH

AF:

0.00206

GnomAD3 exomes

AF:

0.284

AC:

15253

AN:

53648

Hom.:

AF XY:

0.295

AC XY:

8574

AN XY:

29028

show subpopulations

Gnomad AFR exome

AF:

0.120

Gnomad AMR exome

AF:

0.310

Gnomad ASJ exome

AF:

0.310

Gnomad EAS exome

AF:

0.305

Gnomad SAS exome

AF:

0.344

Gnomad FIN exome

AF:

0.264

Gnomad NFE exome

AF:

0.272

Gnomad OTH exome

AF:

0.284

GnomAD4 exome

AF:

0.100

AC:

77264

AN:

769476

Hom.:

Cov.:

AF XY:

0.104

AC XY:

39973

AN XY:

383598

show subpopulations

Gnomad4 AFR exome

AF:

0.0328

Gnomad4 AMR exome

AF:

0.176

Gnomad4 ASJ exome

AF:

0.126

Gnomad4 EAS exome

AF:

0.170

Gnomad4 SAS exome

AF:

0.175

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.0916

Gnomad4 OTH exome

AF:

0.102

GnomAD4 genome

AF:

0.00444

AC:

467

AN:

105118

Hom.:

Cov.:

AF XY:

0.00467

AC XY:

237

AN XY:

50700

show subpopulations

Gnomad4 AFR

AF:

0.00128

Gnomad4 AMR

AF:

0.00587

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00134

Gnomad4 SAS

AF:

0.00240

Gnomad4 FIN

AF:

0.00848

Gnomad4 NFE

AF:

0.00562

Gnomad4 OTH

AF:

0.00205

Alfa

AF:

0.00242

Hom.:

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 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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