chr3-142046814-A-T

Variant names:

• chr3-142046814-A-T
• rs11720300
• NM_001178139.2:c.83-41270T>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.83-41270T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0568 in 152,030 control chromosomes in the GnomAD database, including 304 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 0.057 (304 hom., cov: 32)
• Consequence: TFDP2 NM_001178139.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001178139.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TFDP2	NM_001178139.2	MANE Select	c.83-41270T>A		intron	N/A	NP_001171610.1
	TFDP2	NM_001375773.1		c.83-41270T>A		intron	N/A	NP_001362702.1
	TFDP2	NM_001375775.1		c.-87-41270T>A		intron	N/A	NP_001362704.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TFDP2	ENST00000489671.6	TSL:1 MANE Select	c.83-41270T>A		intron	N/A	ENSP00000420616.1
	TFDP2	ENST00000467072.5	TSL:1	c.-102+7301T>A		intron	N/A	ENSP00000418590.1
	TFDP2	ENST00000494358.5	TSL:1	c.-101-41270T>A		intron	N/A	ENSP00000420657.1

Frequencies

GnomAD3 genomes AF: 0.0568 AC: 8636 AN: 151912 Hom.: 304 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0690

Gnomad EAS AF: 0.0417

Gnomad SAS AF: 0.0473

Gnomad FIN AF: 0.0330

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0864

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0568 AC: 8633 AN: 152030 Hom.: 304 Cov.: 32 AF XY: 0.0536 AC XY: 3980 AN XY: 74308

African (AFR) AF: 0.0159 AC: 660 AN: 41448

American (AMR) AF: 0.0561 AC: 856 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0690 AC: 239 AN: 3464

East Asian (EAS) AF: 0.0416 AC: 215 AN: 5170

South Asian (SAS) AF: 0.0476 AC: 229 AN: 4814

European-Finnish (FIN) AF: 0.0330 AC: 349 AN: 10572

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0864 AC: 5876 AN: 67990

Other (OTH) AF: 0.0601 AC: 127 AN: 2112

Alfa AF: 0.0660 Hom.: 40

Bravo AF: 0.0564

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.7
DANN	Benign	0.82
PhyloP100		-0.090
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: rs11720300; hg19: chr3-141765656;