rs2129107

Variant names:

• chr9-81734706-T-C
• rs2129107
• ENST00000437181.2:n.248-13262T>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.248-13262T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,016 control chromosomes in the GnomAD database, including 36,036 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 0.68 (36036 hom., cov: 32)
• Consequence: TLE1-DT ENST00000437181.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 4 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLE1-DT	NR_109772.1	n.248-13262T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TLE1-DT	ENST00000437181.2	n.248-13262T>C		intron_variant	Intron 1 of 3	1
TLE1-DT	ENST00000769780.1	n.146-13262T>C		intron_variant	Intron 1 of 3
TLE1-DT	ENST00000769781.1	n.132-4147T>C		intron_variant	Intron 1 of 4
TLE1-DT	ENST00000769782.1	n.132-4147T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103386 AN: 151898 Hom.: 35985 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.681 AC: 103497 AN: 152016 Hom.: 36036 Cov.: 32 AF XY: 0.675 AC XY: 50169 AN XY: 74280

African (AFR) AF: 0.829 AC: 34407 AN: 41500

American (AMR) AF: 0.650 AC: 9925 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2413 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2454 AN: 5132

South Asian (SAS) AF: 0.629 AC: 3033 AN: 4820

European-Finnish (FIN) AF: 0.592 AC: 6244 AN: 10540

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42774 AN: 67978

Other (OTH) AF: 0.682 AC: 1440 AN: 2112

Alfa AF: 0.652 Hom.: 6580

Bravo AF: 0.691

Asia WGS AF: 0.576 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.7
DANN	Benign	0.34
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2129107; hg19: chr9-84349621;