rs11139399

chr9-81757826-T-C

Variant summary

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

The NR_109772.1(TLE1-DT):n.486+8014T>C variant causes a intron, non coding transcript 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 NR_109772.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLE1-DT	NR_109772.1	n.486+8014T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLE1-DT	ENST00000437181.2	n.486+8014T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.458

Alfa AF: 0.430 Hom.: 13535

Bravo AF: 0.489

Asia WGS AF: 0.383 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	6.5
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11139399; hg19: chr9-84372741;