Variant 5-168062044-CTTT-CTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001395460.1(TENM2):c.1310-4del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 4739 hom., cov: 0)

Exomes 𝑓: 0.23 ( 13185 hom. )

Consequence

TENM2
NM_001395460.1 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.806

Variant links:

Genes affected

TENM2 (HGNC:29943): (teneurin transmembrane protein 2) Enables cell adhesion molecule binding activity and signaling receptor binding activity. Involved in several processes, including calcium-mediated signaling using intracellular calcium source; heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules; and retrograde trans-synaptic signaling by trans-synaptic protein complex. Located in cell-cell junction and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TENM2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM2	NM_001395460.1 linkuse as main transcript	c.1310-4del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000518659.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM2	ENST00000518659.6 linkuse as main transcript	c.1310-4del		splice_polypyrimidine_tract_variant, intron_variant		5	NM_001395460.1	P1	Q9NT68-1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

36154

AN:

146920

Hom.:

4727

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.411

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.229

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.342

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.248

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.224

GnomAD4 exome

AF:

0.226

AC:

293538

AN:

1300740

Hom.:

13185

Cov.:

AF XY:

0.228

AC XY:

147249

AN XY:

646646

show subpopulations

Gnomad4 AFR exome

AF:

0.321

Gnomad4 AMR exome

AF:

0.193

Gnomad4 ASJ exome

AF:

0.230

Gnomad4 EAS exome

AF:

0.404

Gnomad4 SAS exome

AF:

0.311

Gnomad4 FIN exome

AF:

0.227

Gnomad4 NFE exome

AF:

0.211

Gnomad4 OTH exome

AF:

0.240

GnomAD4 genome

AF:

0.246

AC:

36190

AN:

146968

Hom.:

4739

Cov.:

AF XY:

0.246

AC XY:

17536

AN XY:

71294

show subpopulations

Gnomad4 AFR

AF:

0.309

Gnomad4 AMR

AF:

0.151

Gnomad4 ASJ

AF:

0.229

Gnomad4 EAS

AF:

0.449

Gnomad4 SAS

AF:

0.344

Gnomad4 FIN

AF:

0.227

Gnomad4 NFE

AF:

0.209

Gnomad4 OTH

AF:

0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over