rs9577581

Positions:

• chr13-113597687-G-A
• chr13-113597687-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000375370.10(TFDP1):​c.12+11838G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,166 control chromosomes in the GnomAD database, including 3,549 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 0.18 (3549 hom., cov: 33)
• Consequence: TFDP1 ENST00000375370.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

Genes affected

TFDP1 (HGNC:11749): (transcription factor Dp-1) This gene encodes a member of a family of transcription factors that heterodimerize with E2F proteins to enhance their DNA-binding activity and promote transcription from E2F target genes. The encoded protein functions as part of this complex to control the transcriptional activity of numerous genes involved in cell cycle progression from G1 to S phase. Alternative splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 1, 15, and X.[provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TFDP1	NM_007111.5	c.12+11838G>A		intron_variant		ENST00000375370.10	NP_009042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TFDP1	ENST00000375370.10	c.12+11838G>A		intron_variant		1	NM_007111.5	ENSP00000364519	P1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27643 AN: 152048 Hom.: 3549 Cov.: 33

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.182 AC: 27642 AN: 152166 Hom.: 3549 Cov.: 33 AF XY: 0.196 AC XY: 14550 AN XY: 74372

Gnomad4 AFR AF: 0.0382

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.165

Alfa AF: 0.204 Hom.: 4390

Bravo AF: 0.158

Asia WGS AF: 0.337 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.56

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

Publications

LitVar

Other links and lift over

dbSNP: rs9577581; hg19: chr13-114252002;