Variant 5-167284857-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001395460.1(TENM2):c.20G>A(p.Arg7Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0064 in 1,551,342 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0066 ( 41 hom. )

Consequence

TENM2
NM_001395460.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 9.60

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:

TENM2 (HGNC:):

TENM2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008473635).

BP6

Variant 5-167284857-G-A is Benign according to our data. Variant chr5-167284857-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2656025.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 709 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM2	NM_001395460.1 linkuse as main transcript	c.20G>A	p.Arg7Gln	missense_variant	3/31	ENST00000518659.6	NP_001382389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM2	ENST00000518659.6 linkuse as main transcript	c.20G>A	p.Arg7Gln	missense_variant	3/31	5	NM_001395460.1	ENSP00000429430.1		Q9NT68-1
TENM2	ENST00000695884.1 linkuse as main transcript	n.672G>A		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes

AF:

0.00467

AC:

710

AN:

152082

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00123

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00419

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00160

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00795

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00432

AC:

679

AN:

157014

Hom.:

AF XY:

0.00461

AC XY:

383

AN XY:

83076

show subpopulations

Gnomad AFR exome

AF:

0.000993

Gnomad AMR exome

AF:

0.00142

Gnomad ASJ exome

AF:

0.00447

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00290

Gnomad FIN exome

AF:

0.00213

Gnomad NFE exome

AF:

0.00768

Gnomad OTH exome

AF:

0.00657

GnomAD4 exome

AF:

0.00659

AC:

9218

AN:

1399142

Hom.:

Cov.:

AF XY:

0.00651

AC XY:

4494

AN XY:

690044

show subpopulations

Gnomad4 AFR exome

AF:

0.000855

Gnomad4 AMR exome

AF:

0.00143

Gnomad4 ASJ exome

AF:

0.00461

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00325

Gnomad4 FIN exome

AF:

0.00203

Gnomad4 NFE exome

AF:

0.00773

Gnomad4 OTH exome

AF:

0.00531

GnomAD4 genome

AF:

0.00466

AC:

709

AN:

152200

Hom.:

Cov.:

AF XY:

0.00466

AC XY:

347

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.00123

Gnomad4 AMR

AF:

0.00419

Gnomad4 ASJ

AF:

0.00576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00160

Gnomad4 NFE

AF:

0.00794

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00741

Hom.:

Bravo

AF:

0.00467

TwinsUK

AF:

0.00458

AC:

ALSPAC

AF:

0.00597

AC:

ExAC

AF:

0.00414

AC:

106

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

TENM2: PP2, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Uncertain

0.080

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.0028

Eigen

Pathogenic

0.78

Eigen_PC

Pathogenic

0.78

FATHMM_MKL

Uncertain

0.96

LIST_S2

Uncertain

0.91

M_CAP

Pathogenic

0.49

MetaRNN

Benign

0.0085

MetaSVM

Uncertain

0.54

MutationAssessor

Benign

2.0

PrimateAI

Uncertain

0.78

PROVEAN

Benign

-0.79

REVEL

Uncertain

0.58

Sift

Uncertain

0.011

Sift4G

Benign

0.070

Polyphen

0.99

Vest4

0.31

MVP

0.32

MPC

1.2

ClinPred

0.036

GERP RS

5.2

Varity_R

0.24

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over