3-142100008-C-T

Position:

• chr3-142100008-C-T

Variant summary

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

The NM_001178139.2(TFDP2):​c.15+1727G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,018 control chromosomes in the GnomAD database, including 3,196 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 0.20 (3196 hom., cov: 32)
• Consequence: TFDP2 NM_001178139.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TFDP2	NM_001178139.2	c.15+1727G>A		intron_variant		ENST00000489671.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TFDP2	ENST00000489671.6	c.15+1727G>A		intron_variant		1	NM_001178139.2	P3

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30975 AN: 151900 Hom.: 3189 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.204 AC: 31013 AN: 152018 Hom.: 3196 Cov.: 32 AF XY: 0.201 AC XY: 14940 AN XY: 74298

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.196

Alfa AF: 0.194 Hom.: 4330

Bravo AF: 0.207

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.38
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11705932; hg19: chr3-141818850;