rs8050135

Variant names:

• chr16-71438668-T-C
• rs8050135
• NM_001367365.2:c.-97+3301A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367365.2. 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
	TLE7	NM_001367365.2	MANE Select	c.-97+3301A>G		intron	N/A	NP_001354294.1	A0A1W2PR48

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLE7	ENST00000561754.4	TSL:5 MANE Select	c.-97+3301A>G		intron	N/A	ENSP00000492311.2	A0A1W2PR48

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

African (AFR) AF: 0.803 AC: 25984 AN: 32378

American (AMR) AF: 0.395 AC: 4348 AN: 11014

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1082 AN: 3280

East Asian (EAS) AF: 0.00596 AC: 25 AN: 4192

South Asian (SAS) AF: 0.145 AC: 552 AN: 3814

European-Finnish (FIN) AF: 0.391 AC: 2415 AN: 6174

Middle Eastern (MID) AF: 0.537 AC: 130 AN: 242

European-Non Finnish (NFE) AF: 0.416 AC: 25954 AN: 62450

Other (OTH) AF: 0.460 AC: 789 AN: 1714

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.064
DANN	Benign	0.071
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs8050135; hg19: chr16-71472571;