ENST00000437181.2:n.248-10936G>A

Variant names:

• chr9-81737032-G-A
• rs9314704
• ENST00000437181.2:n.248-10936G>A

Variant summary

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

The ENST00000437181.2(TLE1-DT):​n.248-10936G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,082 control chromosomes in the GnomAD database, including 32,824 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 0.65 (32824 hom., cov: 32)
• Consequence: TLE1-DT ENST00000437181.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 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.248-10936G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLE1-DT	ENST00000437181.2	TSL:1	n.248-10936G>A		intron	N/A
	TLE1-DT	ENST00000769780.1		n.146-10936G>A		intron	N/A
	TLE1-DT	ENST00000769781.1		n.132-1821G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98661 AN: 151964 Hom.: 32772 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.649 AC: 98770 AN: 152082 Hom.: 32824 Cov.: 32 AF XY: 0.647 AC XY: 48105 AN XY: 74322

African (AFR) AF: 0.794 AC: 32948 AN: 41500

American (AMR) AF: 0.607 AC: 9282 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2254 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2526 AN: 5162

South Asian (SAS) AF: 0.606 AC: 2925 AN: 4830

European-Finnish (FIN) AF: 0.593 AC: 6258 AN: 10560

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40500 AN: 67960

Other (OTH) AF: 0.643 AC: 1357 AN: 2110

Alfa AF: 0.623 Hom.: 6168

Bravo AF: 0.657

Asia WGS AF: 0.557 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.39
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs9314704; hg19: chr9-84351947;