3-142106756-C-T

Variant names:

• chr3-142106756-C-T
• rs6773343
• NM_001178139.2:c.-92-4915G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The NM_001178139.2(TFDP2):​c.-92-4915G>A variant causes a intron change. The variant allele was found at a frequency of 0.74 in 152,110 control chromosomes in the GnomAD database, including 41,692 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 0.74 (41692 hom., cov: 33)
• Consequence: TFDP2 NM_001178139.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.60
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TFDP2	NM_001178139.2	c.-92-4915G>A		intron_variant	Intron 1 of 12	ENST00000489671.6	NP_001171610.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TFDP2	ENST00000489671.6	c.-92-4915G>A		intron_variant	Intron 1 of 12	1	NM_001178139.2	ENSP00000420616.1

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112535 AN: 151992 Hom.: 41670 Cov.: 33

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.750

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.740 AC: 112604 AN: 152110 Hom.: 41692 Cov.: 33 AF XY: 0.745 AC XY: 55363 AN XY: 74360

African (AFR) AF: 0.730 AC: 30279 AN: 41468

American (AMR) AF: 0.783 AC: 11961 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2892 AN: 3470

East Asian (EAS) AF: 0.727 AC: 3770 AN: 5186

South Asian (SAS) AF: 0.810 AC: 3907 AN: 4822

European-Finnish (FIN) AF: 0.748 AC: 7909 AN: 10576

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.726 AC: 49342 AN: 67998

Other (OTH) AF: 0.752 AC: 1589 AN: 2114

Alfa AF: 0.679 Hom.: 2783

Bravo AF: 0.743

Asia WGS AF: 0.795 AC: 2766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	21
DANN	Benign	0.81
PhyloP100		4.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6773343; hg19: chr3-141825598;