Genetic Variant TFDP1:p.Leu42Leu (chr13-113623226-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_007111.5(TFDP1):c.126C>T(p.Leu42Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00569 in 1,613,614 control chromosomes in the GnomAD database, including 287 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 0.011 ( 40 hom., cov: 33)

Exomes 𝑓: 0.0052 ( 247 hom. )

Consequence

TFDP1
NM_007111.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62

Publications

7 publications found

Variant links:

Genes affected

TFDP1 (HGNC:11749): (transcription factor Dp-1) This gene encodes a member of a family of transcription factors that heterodimerize with E2F proteins to enhance their DNA-binding activity and promote transcription from E2F target genes. The encoded protein functions as part of this complex to control the transcriptional activity of numerous genes involved in cell cycle progression from G1 to S phase. Alternative splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 1, 15, and X.[provided by RefSeq, Jan 2009]

TFDP1 links:

LOC124903219 (HGNC:):

LOC124903219 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP7

Synonymous conserved (PhyloP=-1.62 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TFDP1	NM_007111.5 link	c.126C>T	p.Leu42Leu	synonymous_variant	Exon 4 of 12	ENST00000375370.10	NP_009042.1	Q14186-1A0A024RDY4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TFDP1	ENST00000375370.10 link	c.126C>T	p.Leu42Leu	synonymous_variant	Exon 4 of 12	1	NM_007111.5	ENSP00000364519.4		Q14186-1

Frequencies

GnomAD3 genomes

AF:

0.0105

AC:

1604

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0159

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.00635

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.0139

Gnomad FIN

AF:

0.00424

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00220

Gnomad OTH

AF:

0.0110

GnomAD2 exomes

AF:

0.0129

AC:

3227

AN:

250020

AF XY:

0.0122

show subpopulations

Gnomad AFR exome

AF:

0.0154

Gnomad AMR exome

AF:

0.00215

Gnomad ASJ exome

AF:

0.000399

Gnomad EAS exome

AF:

0.123

Gnomad FIN exome

AF:

0.00338

Gnomad NFE exome

AF:

0.00187

Gnomad OTH exome

AF:

0.00786

GnomAD4 exome

AF:

0.00518

AC:

7563

AN:

1461288

Hom.:

247

Cov.:

AF XY:

0.00529

AC XY:

3844

AN XY:

726852

show subpopulations

African (AFR)

AF:

0.0170

AC:

569

AN:

33460

American (AMR)

AF:

0.00215

AC:

AN:

44678

Ashkenazi Jewish (ASJ)

AF:

0.000498

AC:

AN:

26116

East Asian (EAS)

AF:

0.0889

AC:

3525

AN:

39660

South Asian (SAS)

AF:

0.0104

AC:

899

AN:

86076

European-Finnish (FIN)

AF:

0.00311

AC:

166

AN:

53388

Middle Eastern (MID)

AF:

0.00468

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00138

AC:

1539

AN:

1111772

Other (OTH)

AF:

0.0121

AC:

729

AN:

60370

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

362

724

1085

1447

1809

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

256

384

512

640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0106

AC:

1621

AN:

152326

Hom.:

Cov.:

AF XY:

0.0110

AC XY:

818

AN XY:

74478

show subpopulations

African (AFR)

AF:

0.0162

AC:

674

AN:

41578

American (AMR)

AF:

0.00634

AC:

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.000288

AC:

AN:

3472

East Asian (EAS)

AF:

0.107

AC:

552

AN:

5182

South Asian (SAS)

AF:

0.0137

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00424

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00220

AC:

150

AN:

68028

Other (OTH)

AF:

0.0128

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

160

240

320

400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00508

Hom.:

Bravo

AF:

0.0118

Asia WGS

AF:

0.0520

AC:

180

AN:

3478

EpiCase

AF:

0.00322

EpiControl

AF:

0.00237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.52

(source)

DANN

Benign

0.63

PhyloP100

-1.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=279/21

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over