Variant rs2902101 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001395460.1(TENM2):c.-190+42151C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,016 control chromosomes in the GnomAD database, including 12,612 homozygotes. 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 0.39 ( 12612 hom., cov: 32)

Consequence

TENM2
NM_001395460.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.198

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM2	NM_001395460.1 link	c.-190+42151C>A		intron_variant		ENST00000518659.6	NP_001382389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM2	ENST00000518659.6 link	c.-190+42151C>A		intron_variant		5	NM_001395460.1	ENSP00000429430.1		Q9NT68-1
TENM2	ENST00000695884.1 link	n.463+42151C>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58558

AN:

151896

Hom.:

12604

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.465

Gnomad AMR

AF:

0.543

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.420

Gnomad SAS

AF:

0.537

Gnomad FIN

AF:

0.560

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.432

Gnomad OTH

AF:

0.384

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

GnomAD4 genome

AF:

0.385

AC:

58591

AN:

152016

Hom.:

12612

Cov.:

AF XY:

0.397

AC XY:

29485

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.188

Gnomad4 AMR

AF:

0.544

Gnomad4 ASJ

AF:

0.326

Gnomad4 EAS

AF:

0.420

Gnomad4 SAS

AF:

0.537

Gnomad4 FIN

AF:

0.560

Gnomad4 NFE

AF:

0.432

Gnomad4 OTH

AF:

0.384

Alfa

AF:

0.420

Hom.:

17799

Bravo

AF:

0.375

Asia WGS

AF:

0.474

AC:

1645

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.4

DANN

Benign

0.53

Splicing

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