rs8050135

Positions:

• chr16-71438668-T-C
• chr16-71438668-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367365.2(TLE7):​c.-97+3301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.49 (17390 hom., cov: 17)
• Consequence: TLE7 NM_001367365.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.46

Genes affected

TLE7 (HGNC:53648): (TLE family member 7) Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of canonical Wnt signaling pathway. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLE7	NM_001367365.2	c.-97+3301A>G		intron_variant		ENST00000561754.4	NP_001354294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLE7	ENST00000561754.4	c.-97+3301A>G		intron_variant		5	NM_001367365.2	ENSP00000492311	P1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 61734 AN: 126062 Hom.: 17373 Cov.: 17

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.00618

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.490 AC: 61764 AN: 126088 Hom.: 17390 Cov.: 17 AF XY: 0.487 AC XY: 28897 AN XY: 59324

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.00596

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.460

Alfa AF: 0.438 Hom.: 1805

Bravo AF: 0.495

Asia WGS AF: 0.145 AC: 506 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.064
DANN	Benign	0.071

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8050135; hg19: chr16-71472571;