rs9577581

Variant names:

• chr13-113597687-G-A
• rs9577581
• NM_007111.5:c.12+11838G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_007111.5(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 NM_007111.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TFDP1	NM_007111.5	c.12+11838G>A		intron_variant	Intron 2 of 11	ENST00000375370.10	NP_009042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TFDP1	ENST00000375370.10	c.12+11838G>A		intron_variant	Intron 2 of 11	1	NM_007111.5	ENSP00000364519.4

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

African (AFR) AF: 0.0382 AC: 1588 AN: 41568

American (AMR) AF: 0.160 AC: 2446 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3468

East Asian (EAS) AF: 0.417 AC: 2146 AN: 5150

South Asian (SAS) AF: 0.351 AC: 1693 AN: 4824

European-Finnish (FIN) AF: 0.408 AC: 4313 AN: 10570

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14539 AN: 67982

Other (OTH) AF: 0.165 AC: 348 AN: 2112

Alfa AF: 0.198 Hom.: 5367

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
PhyloP100		0.20
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: rs9577581; hg19: chr13-114252002;