rs347685

Positions:

• chr3-142088295-C-A
• chr3-142088295-C-G

Variant summary

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

The NM_001178139.2(TFDP2):​c.82+4766G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 151,996 control chromosomes in the GnomAD database, including 42,224 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 0.75 (42224 hom., cov: 31)
• Consequence: TFDP2 NM_001178139.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461

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]

TFDP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TFDP2	NM_001178139.2	c.82+4766G>T		intron_variant		ENST00000489671.6	NP_001171610.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TFDP2	ENST00000489671.6	c.82+4766G>T		intron_variant		1	NM_001178139.2	ENSP00000420616.1

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113209 AN: 151878 Hom.: 42201 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.745 AC: 113280 AN: 151996 Hom.: 42224 Cov.: 31 AF XY: 0.749 AC XY: 55678 AN XY: 74290

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.757

Alfa AF: 0.734 Hom.: 68544

Bravo AF: 0.749

Asia WGS AF: 0.796 AC: 2769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs347685; hg19: chr3-141807137;