chr3-142021234-G-A

Variant names:

• chr3-142021234-G-A
• rs733996
• NM_001178139.2:c.83-15690C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001178139.2(TFDP2):​c.83-15690C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.046 in 152,212 control chromosomes in the GnomAD database, including 166 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 0.046 (166 hom., cov: 32)
• Consequence: TFDP2 NM_001178139.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 5 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TFDP2	NM_001178139.2	c.83-15690C>T		intron_variant	Intron 3 of 12	ENST00000489671.6	NP_001171610.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TFDP2	ENST00000489671.6	c.83-15690C>T		intron_variant	Intron 3 of 12	1	NM_001178139.2	ENSP00000420616.1

Frequencies

GnomAD3 genomes AF: 0.0461 AC: 7012 AN: 152094 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.0446

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0698

Gnomad FIN AF: 0.0500

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0524

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0460 AC: 7006 AN: 152212 Hom.: 166 Cov.: 32 AF XY: 0.0459 AC XY: 3414 AN XY: 74416

African (AFR) AF: 0.0445 AC: 1848 AN: 41534

American (AMR) AF: 0.0345 AC: 527 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3468

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5180

South Asian (SAS) AF: 0.0701 AC: 338 AN: 4822

European-Finnish (FIN) AF: 0.0500 AC: 530 AN: 10592

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0524 AC: 3562 AN: 68006

Other (OTH) AF: 0.0444 AC: 94 AN: 2116

Alfa AF: 0.0508 Hom.: 408

Bravo AF: 0.0440

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.54
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs733996; hg19: chr3-141740076;