NM_001178139.2:c.83-19565G>A

Variant names:

• chr3-142025109-C-T
• rs7644383
• NM_001178139.2:c.83-19565G>A

Variant summary

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

The NM_001178139.2(TFDP2):​c.83-19565G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,004 control chromosomes in the GnomAD database, including 49,896 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 0.81 (49896 hom., cov: 31)
• Consequence: TFDP2 NM_001178139.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TFDP2	NM_001178139.2	c.83-19565G>A		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.83-19565G>A		intron_variant	Intron 3 of 12	1	NM_001178139.2	ENSP00000420616.1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122353 AN: 151886 Hom.: 49833 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.806 AC: 122475 AN: 152004 Hom.: 49896 Cov.: 31 AF XY: 0.809 AC XY: 60085 AN XY: 74274

African (AFR) AF: 0.936 AC: 38848 AN: 41486

American (AMR) AF: 0.820 AC: 12531 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2897 AN: 3470

East Asian (EAS) AF: 0.779 AC: 4028 AN: 5174

South Asian (SAS) AF: 0.810 AC: 3906 AN: 4820

European-Finnish (FIN) AF: 0.747 AC: 7824 AN: 10470

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49753 AN: 67988

Other (OTH) AF: 0.808 AC: 1705 AN: 2110

Alfa AF: 0.753 Hom.: 53276

Bravo AF: 0.819

Asia WGS AF: 0.824 AC: 2857 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.33
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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: rs7644383; hg19: chr3-141743951;