rs11705932

Variant names:

• chr3-142100008-C-T
• rs11705932
• NM_001178139.2:c.15+1727G>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.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
• Publications: 15 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=-0.86).
• 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 rank	MANE	Protein	UniProt
TFDP2	NM_001178139.2	c.15+1727G>A		intron_variant	Intron 2 of 12	ENST00000489671.6	NP_001171610.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TFDP2	ENST00000489671.6	c.15+1727G>A		intron_variant	Intron 2 of 12	1	NM_001178139.2	ENSP00000420616.1

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

African (AFR) AF: 0.240 AC: 9930 AN: 41442

American (AMR) AF: 0.176 AC: 2685 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 428 AN: 3460

East Asian (EAS) AF: 0.268 AC: 1380 AN: 5158

South Asian (SAS) AF: 0.119 AC: 573 AN: 4816

European-Finnish (FIN) AF: 0.175 AC: 1850 AN: 10560

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13542 AN: 67996

Other (OTH) AF: 0.196 AC: 414 AN: 2110

Alfa AF: 0.196 Hom.: 5999

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
PhyloP100		-1.2
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: rs11705932; hg19: chr3-141818850;