3-141944841-C-T

Variant names:

• chr3-141944841-C-T
• rs1045279
• NM_001178139.2:c.*7672G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001178139.2(TFDP2):​c.*7672G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,254 control chromosomes in the GnomAD database, including 60,031 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 0.89 (60030 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: TFDP2 NM_001178139.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TFDP2	NM_001178139.2	MANE Select	c.*7672G>A		3_prime_UTR	Exon 13 of 13	NP_001171610.1	Q14188-1
	TFDP2	NM_001375773.1		c.*7672G>A		3_prime_UTR	Exon 13 of 13	NP_001362702.1
	TFDP2	NM_001375774.1		c.*7672G>A		3_prime_UTR	Exon 11 of 11	NP_001362703.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TFDP2	ENST00000489671.6	TSL:1 MANE Select	c.*7672G>A		3_prime_UTR	Exon 13 of 13	ENSP00000420616.1	Q14188-1
	TFDP2	ENST00000499676.5	TSL:1	c.*7672G>A		3_prime_UTR	Exon 10 of 10	ENSP00000439782.2	Q14188-8

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134873 AN: 152134 Hom.: 59976 Cov.: 33

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.873

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.887 AC: 134985 AN: 152252 Hom.: 60030 Cov.: 33 AF XY: 0.887 AC XY: 66029 AN XY: 74434

African (AFR) AF: 0.968 AC: 40263 AN: 41576

American (AMR) AF: 0.863 AC: 13186 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3089 AN: 3472

East Asian (EAS) AF: 0.912 AC: 4718 AN: 5176

South Asian (SAS) AF: 0.860 AC: 4148 AN: 4824

European-Finnish (FIN) AF: 0.836 AC: 8852 AN: 10588

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57814 AN: 68016

Other (OTH) AF: 0.874 AC: 1849 AN: 2116

Alfa AF: 0.871 Hom.: 7181

Bravo AF: 0.894

Asia WGS AF: 0.875 AC: 3042 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	7.3
DANN	Benign	0.80
PhyloP100		0.029
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs1045279; hg19: chr3-141663683;