chr3-142014575-G-T

Variant names:

• chr3-142014575-G-T
• rs6781340
• NM_001178139.2:c.83-9031C>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.83-9031C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,780 control chromosomes in the GnomAD database, including 29,932 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 0.61 (29932 hom., cov: 30)
• Consequence: TFDP2 NM_001178139.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TFDP2	NM_001178139.2	c.83-9031C>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.83-9031C>A		intron_variant	Intron 3 of 12	1	NM_001178139.2	ENSP00000420616.1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 92972 AN: 151662 Hom.: 29912 Cov.: 30

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.613 AC: 93014 AN: 151780 Hom.: 29932 Cov.: 30 AF XY: 0.620 AC XY: 45981 AN XY: 74162

African (AFR) AF: 0.386 AC: 15955 AN: 41298

American (AMR) AF: 0.722 AC: 11019 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2820 AN: 3468

East Asian (EAS) AF: 0.776 AC: 3997 AN: 5152

South Asian (SAS) AF: 0.732 AC: 3527 AN: 4820

European-Finnish (FIN) AF: 0.699 AC: 7349 AN: 10518

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46015 AN: 67952

Other (OTH) AF: 0.659 AC: 1387 AN: 2104

Alfa AF: 0.519 Hom.: 1692

Bravo AF: 0.608

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.56
PhyloP100		-0.69
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: rs6781340; hg19: chr3-141733417;