chr3-141950843-A-G

Variant names:

• chr3-141950843-A-G
• rs11569291
• NM_001178139.2:c.*1670T>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.*1670T>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 0.0741 in 152,500 control chromosomes in the GnomAD database, including 528 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 0.074 (527 hom., cov: 32)
  • Exomes 𝑓: 0.071 (1 hom.)
• Consequence: TFDP2 NM_001178139.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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.*1670T>C		3_prime_UTR	Exon 13 of 13	NP_001171610.1
	TFDP2	NM_001375773.1		c.*1670T>C		3_prime_UTR	Exon 13 of 13	NP_001362702.1
	TFDP2	NM_001375774.1		c.*1670T>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.*1670T>C		3_prime_UTR	Exon 13 of 13	ENSP00000420616.1
	TFDP2	ENST00000499676.5	TSL:1	c.*1670T>C		3_prime_UTR	Exon 10 of 10	ENSP00000439782.2

Frequencies

GnomAD3 genomes AF: 0.0742 AC: 11285 AN: 152170 Hom.: 527 Cov.: 32

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0737

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0484

Gnomad FIN AF: 0.0727

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0755

GnomAD4 exome AF: 0.0708 AC: 15 AN: 212 Hom.: 1 Cov.: 0 AF XY: 0.0530 AC XY: 7 AN XY: 132

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: 0.0686 AC: 14 AN: 204

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0741 AC: 11286 AN: 152288 Hom.: 527 Cov.: 32 AF XY: 0.0711 AC XY: 5296 AN XY: 74470

African (AFR) AF: 0.0205 AC: 851 AN: 41572

American (AMR) AF: 0.0728 AC: 1114 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0737 AC: 256 AN: 3472

East Asian (EAS) AF: 0.0618 AC: 320 AN: 5180

South Asian (SAS) AF: 0.0489 AC: 236 AN: 4830

European-Finnish (FIN) AF: 0.0727 AC: 771 AN: 10608

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7501 AN: 68012

Other (OTH) AF: 0.0742 AC: 157 AN: 2116

Alfa AF: 0.0893 Hom.: 1096

Bravo AF: 0.0725

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.48
DANN	Benign	0.40
PhyloP100		0.082
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: rs11569291; hg19: chr3-141669685;