NM_001178139.2:c.*7603T>C

Variant names:

• chr3-141944910-A-G
• rs9942
• NM_001178139.2:c.*7603T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001178139.2(TFDP2):​c.*7603T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,286 control chromosomes in the GnomAD database, including 58,178 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 0.87 (58178 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: TFDP2 NM_001178139.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 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.*7603T>C		3_prime_UTR	Exon 13 of 13	NP_001171610.1
	TFDP2	NM_001375773.1		c.*7603T>C		3_prime_UTR	Exon 13 of 13	NP_001362702.1
	TFDP2	NM_001375774.1		c.*7603T>C		3_prime_UTR	Exon 11 of 11	NP_001362703.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TFDP2	ENST00000489671.6	TSL:1 MANE Select	c.*7603T>C		3_prime_UTR	Exon 13 of 13	ENSP00000420616.1
	TFDP2	ENST00000499676.5	TSL:1	c.*7603T>C		3_prime_UTR	Exon 10 of 10	ENSP00000439782.2

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132919 AN: 152168 Hom.: 58127 Cov.: 34

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.866

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.874 AC: 133028 AN: 152286 Hom.: 58178 Cov.: 34 AF XY: 0.875 AC XY: 65152 AN XY: 74456

African (AFR) AF: 0.923 AC: 38353 AN: 41570

American (AMR) AF: 0.859 AC: 13140 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3088 AN: 3472

East Asian (EAS) AF: 0.911 AC: 4727 AN: 5190

South Asian (SAS) AF: 0.860 AC: 4147 AN: 4822

European-Finnish (FIN) AF: 0.836 AC: 8867 AN: 10602

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

European-Non Finnish (NFE) AF: 0.850 AC: 57806 AN: 68014

Other (OTH) AF: 0.867 AC: 1834 AN: 2116

Alfa AF: 0.857 Hom.: 147116

Bravo AF: 0.879

Asia WGS AF: 0.870 AC: 3027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.63
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: rs9942; hg19: chr3-141663752;