rs2796441

Variant names:

• chr9-81694033-G-A
• rs2796441
• ENST00000437181.2:n.247+4074G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-81694033-G-A
• chr9-81694033-G-C
• chr9-81694033-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000437181.2(TLE1-DT):​n.247+4074G>A variant causes a intron 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 ENST00000437181.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.14
• Publications: 102 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLE1-DT	NR_109772.1		n.247+4074G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLE1-DT	ENST00000437181.2	TSL:1	n.247+4074G>A		intron	N/A
	TLE1-DT	ENST00000769780.1		n.145+4074G>A		intron	N/A
	TLE1-DT	ENST00000769781.1		n.131+4074G>A		intron	N/A

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

African (AFR) AF: 0.170 AC: 7058 AN: 41526

American (AMR) AF: 0.451 AC: 6892 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1301 AN: 3472

East Asian (EAS) AF: 0.617 AC: 3184 AN: 5164

South Asian (SAS) AF: 0.438 AC: 2116 AN: 4826

European-Finnish (FIN) AF: 0.427 AC: 4523 AN: 10586

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27258 AN: 67982

Other (OTH) AF: 0.362 AC: 764 AN: 2108

Alfa AF: 0.390 Hom.: 39740

Bravo AF: 0.346

Asia WGS AF: 0.482 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	20
DANN	Benign	0.81
PhyloP100		7.1

Splicing

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

Other links and lift over

dbSNP: rs2796441; hg19: chr9-84308948;