rs11569291

chr3-141950843-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001178139.2(TFDP2):c.*1670T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0741 in 152,500 control chromosomes in the GnomAD database, including 528 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 0.074 (527 hom., cov: 32)
  • Exomes 𝑓: 0.071 (1 hom.)
• Consequence: TFDP2 NM_001178139.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

TFDP2 (HGNC:11751): (transcription factor Dp-2) The gene is a member of the transcription factor DP family. The encoded protein forms heterodimers with the E2F transcription factors resulting in transcriptional activation of cell cycle regulated genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TFDP2	NM_001178139.2	c.*1670T>C		3_prime_UTR_variant	13/13	ENST00000489671.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TFDP2	ENST00000489671.6	c.*1670T>C		3_prime_UTR_variant	13/13	1	NM_001178139.2	P3
TFDP2	ENST00000499676.5	c.*1670T>C		3_prime_UTR_variant	10/10	1

Frequencies

GnomAD3 genomes AF: 0.0742 AC: 11285 AN: 152170 Hom.: 527 Cov.: 32

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0737

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0484

Gnomad FIN AF: 0.0727

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0755

GnomAD4 exome AF: 0.0708 AC: 15 AN: 212 Hom.: 1 Cov.: 0 AF XY: 0.0530 AC XY: 7 AN XY: 132

Gnomad4 FIN exome AF: 0.0686

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0741 AC: 11286 AN: 152288 Hom.: 527 Cov.: 32 AF XY: 0.0711 AC XY: 5296 AN XY: 74470

Gnomad4 AFR AF: 0.0205

Gnomad4 AMR AF: 0.0728

Gnomad4 ASJ AF: 0.0737

Gnomad4 EAS AF: 0.0618

Gnomad4 SAS AF: 0.0489

Gnomad4 FIN AF: 0.0727

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0742

Alfa AF: 0.0985 Hom.: 810

Bravo AF: 0.0725

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.48
Dann	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11569291; hg19: chr3-141669685;