rs2796441

chr9-81694033-G-Achr9-81694033-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_109772.1(TLE1-DT):n.247+4074G>A variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.352 in 152,134 control chromosomes in the GnomAD database, including 10,586 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 0.35 (10586 hom., cov: 33)
• Consequence: TLE1-DT NR_109772.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.14

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLE1-DT	NR_109772.1	n.247+4074G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TLE1-DT	ENST00000437181.2	n.247+4074G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53530 AN: 152016 Hom.: 10584 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.352 AC: 53542 AN: 152134 Hom.: 10586 Cov.: 33 AF XY: 0.360 AC XY: 26745 AN XY: 74376

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.362

Alfa AF: 0.403 Hom.: 25239

Bravo AF: 0.346

Asia WGS AF: 0.482 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
Cadd	Benign	20
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2796441; hg19: chr9-84308948;