rs11139399

Variant names:

• chr9-81757826-T-C
• rs11139399
• ENST00000437181.2:n.486+8014T>C

Variant summary

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

The ENST00000437181.2(TLE1-DT):​n.486+8014T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,110 control chromosomes in the GnomAD database, including 18,476 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 0.48 (18476 hom., cov: 33)
• Consequence: TLE1-DT ENST00000437181.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 7 publications found

Genes affected

TLE1-DT (HGNC:55701): (TLE1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437181.2. 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
	TLE1-DT	NR_109772.1		n.486+8014T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLE1-DT	ENST00000437181.2	TSL:1	n.486+8014T>C		intron	N/A
	TLE1-DT	ENST00000769780.1		n.384+8014T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72737 AN: 151992 Hom.: 18442 Cov.: 33

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.479 AC: 72815 AN: 152110 Hom.: 18476 Cov.: 33 AF XY: 0.474 AC XY: 35228 AN XY: 74350

African (AFR) AF: 0.657 AC: 27284 AN: 41506

American (AMR) AF: 0.398 AC: 6078 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1770 AN: 3466

East Asian (EAS) AF: 0.397 AC: 2050 AN: 5170

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4822

European-Finnish (FIN) AF: 0.399 AC: 4217 AN: 10566

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.415 AC: 28201 AN: 67990

Other (OTH) AF: 0.458 AC: 968 AN: 2112

Alfa AF: 0.447 Hom.: 28977

Bravo AF: 0.489

Asia WGS AF: 0.383 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.5
DANN	Benign	0.89
PhyloP100		0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11139399; hg19: chr9-84372741;