3-141944910-A-G

Position:

• chr3-141944910-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.*7603T>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 0.874 in 152,286 control chromosomes in the GnomAD database, including 58,178 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 0.87 (58178 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: TFDP2 NM_001178139.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TFDP2	NM_001178139.2	c.*7603T>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.*7603T>C		3_prime_UTR_variant	13/13	1	NM_001178139.2	P3
TFDP2	ENST00000499676.5	c.*7603T>C		3_prime_UTR_variant	10/10	1

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132919 AN: 152168 Hom.: 58127 Cov.: 34

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.866

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.874 AC: 133028 AN: 152286 Hom.: 58178 Cov.: 34 AF XY: 0.875 AC XY: 65152 AN XY: 74456

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.867

Alfa AF: 0.853 Hom.: 55807

Bravo AF: 0.879

Asia WGS AF: 0.870 AC: 3027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9942; hg19: chr3-141663752;