Genetic Variant TENM2:c.1310-4delT (chr5-168062044-CT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001395460.1(TENM2):c.1310-4delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. 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_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.806

Publications

1 publications found

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 was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395460.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TENM2	NM_001395460.1	MANE Select	c.1310-4delT	splice_region intron	N/A	NP_001382389.1
TENM2	NM_001122679.2		c.1310-4delT	splice_region intron	N/A	NP_001116151.1
TENM2	NM_001368145.1		c.854-4delT	splice_region intron	N/A	NP_001355074.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TENM2	ENST00000518659.6	TSL:5 MANE Select	c.1310-15delT	intron	N/A	ENSP00000429430.1
TENM2	ENST00000520394.5	TSL:1	c.614-15delT	intron	N/A	ENSP00000427874.1
TENM2	ENST00000519204.5	TSL:5	c.947-15delT	intron	N/A	ENSP00000428964.1

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

GnomAD2 exomes

AF:

0.264

AC:

45396

AN:

172048

AF XY:

0.264

show subpopulations

Gnomad AFR exome

AF:

0.344

Gnomad AMR exome

AF:

0.222

Gnomad ASJ exome

AF:

0.236

Gnomad EAS exome

AF:

0.433

Gnomad FIN exome

AF:

0.237

Gnomad NFE exome

AF:

0.231

Gnomad OTH exome

AF:

0.243

GnomAD4 exome

AF:

0.226

AC:

293538

AN:

1300740

Hom.:

13185

Cov.:

AF XY:

0.228

AC XY:

147249

AN XY:

646646

show subpopulations

African (AFR)

AF:

0.321

AC:

9150

AN:

28488

American (AMR)

AF:

0.193

AC:

6836

AN:

35342

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

5375

AN:

23386

East Asian (EAS)

AF:

0.404

AC:

13572

AN:

33616

South Asian (SAS)

AF:

0.311

AC:

23497

AN:

75526

European-Finnish (FIN)

AF:

0.227

AC:

10619

AN:

46704

Middle Eastern (MID)

AF:

0.240

AC:

912

AN:

3800

European-Non Finnish (NFE)

AF:

0.211

AC:

210665

AN:

1000098

Other (OTH)

AF:

0.240

AC:

12912

AN:

53780

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

10585

21170

31756

42341

52926

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8012

16024

24036

32048

40060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.246

AC:

36190

AN:

146968

Hom.:

4739

Cov.:

AF XY:

0.246

AC XY:

17536

AN XY:

71294

show subpopulations

African (AFR)

AF:

0.309

AC:

12427

AN:

40166

American (AMR)

AF:

0.151

AC:

2233

AN:

14776

Ashkenazi Jewish (ASJ)

AF:

0.229

AC:

792

AN:

3454

East Asian (EAS)

AF:

0.449

AC:

2277

AN:

5066

South Asian (SAS)

AF:

0.344

AC:

1603

AN:

4666

European-Finnish (FIN)

AF:

0.227

AC:

1992

AN:

8786

Middle Eastern (MID)

AF:

0.254

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.209

AC:

13950

AN:

66834

Other (OTH)

AF:

0.232

AC:

471

AN:

2028

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1360

2721

4081

5442

6802

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

394

788

1182

1576

1970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.209

Hom.:

100

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.81

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over