NM_007005.6:c.610-8800T>A

Variant names:

• chr9-79695983-T-A
• rs914715
• NM_007005.6:c.610-8800T>A

Variant summary

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

The NM_007005.6(TLE4):​c.610-8800T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.959 in 152,262 control chromosomes in the GnomAD database, including 70,065 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 0.96 (70065 hom., cov: 30)
• Consequence: TLE4 NM_007005.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 9 publications found

Genes affected

TLE4 (HGNC:11840): (TLE family member 4, transcriptional corepressor) Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of canonical Wnt signaling pathway. Predicted to act upstream of or within Wnt signaling pathway; cellular response to leukemia inhibitory factor; and negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007005.6. 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
	TLE4	NM_007005.6	MANE Select	c.610-8800T>A		intron	N/A	NP_008936.2
	TLE4	NM_001282748.2		c.610-8800T>A		intron	N/A	NP_001269677.1
	TLE4	NM_001351541.2		c.649-8800T>A		intron	N/A	NP_001338470.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLE4	ENST00000376552.8	TSL:1 MANE Select	c.610-8800T>A		intron	N/A	ENSP00000365735.2
	TLE4	ENST00000376537.8	TSL:1	c.610-8800T>A		intron	N/A	ENSP00000365720.4
	TLE4	ENST00000376544.7	TSL:1	c.610-8800T>A		intron	N/A	ENSP00000365727.4

Frequencies

GnomAD3 genomes AF: 0.959 AC: 145911 AN: 152144 Hom.: 70003 Cov.: 30

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.947

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

GnomAD4 genome AF: 0.959 AC: 146032 AN: 152262 Hom.: 70065 Cov.: 30 AF XY: 0.962 AC XY: 71601 AN XY: 74462

African (AFR) AF: 0.988 AC: 41061 AN: 41540

American (AMR) AF: 0.951 AC: 14555 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3224 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5169 AN: 5170

South Asian (SAS) AF: 0.992 AC: 4794 AN: 4832

European-Finnish (FIN) AF: 0.980 AC: 10399 AN: 10614

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63674 AN: 68014

Other (OTH) AF: 0.947 AC: 2001 AN: 2112

Alfa AF: 0.942 Hom.: 37458

Bravo AF: 0.958

Asia WGS AF: 0.994 AC: 3457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.57
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs914715; hg19: chr9-82310898;