dbSNP rs17263582: TENM3:p.Gly1319Gly (chr4-182753544-C-T) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001080477.4(TENM3):c.3957C>T(p.Gly1319Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 1,612,446 control chromosomes in the GnomAD database, including 36,452 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2765 hom., cov: 33)

Exomes 𝑓: 0.21 ( 33687 hom. )

Consequence

TENM3
NM_001080477.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.505

Variant links:

Genes affected

TENM3 (HGNC:29944): (teneurin transmembrane protein 3) This gene encodes a member of the teneurin transmembrane protein family. The encoded protein may be involved in the regulation of neuronal development including development of the visual pathway. Mutations in this gene have been associated with microphthalmia and developmental dysplasia of the hip. [provided by RefSeq, Jan 2023]

TENM3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 4-182753544-C-T is Benign according to our data. Variant chr4-182753544-C-T is described in ClinVar as [Benign]. Clinvar id is 257353.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.505 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENM3	NM_001080477.4 link	c.3957C>T	p.Gly1319Gly	synonymous_variant	Exon 21 of 28	ENST00000511685.6	NP_001073946.1	Q9P273A0A140VJW8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENM3	ENST00000511685.6 link	c.3957C>T	p.Gly1319Gly	synonymous_variant	Exon 21 of 28	5	NM_001080477.4	ENSP00000424226.1		Q9P273
TENM3	ENST00000502950.1 link	n.2365C>T		non_coding_transcript_exon_variant	Exon 14 of 15	2

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27406

AN:

152022

Hom.:

2765

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0881

Gnomad AMI

AF:

0.374

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.209

Gnomad FIN

AF:

0.220

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.225

GnomAD3 exomes

AF:

0.197

AC:

49053

AN:

248714

Hom.:

5274

AF XY:

0.203

AC XY:

27445

AN XY:

134932

show subpopulations

Gnomad AFR exome

AF:

0.0862

Gnomad AMR exome

AF:

0.133

Gnomad ASJ exome

AF:

0.242

Gnomad EAS exome

AF:

0.178

Gnomad SAS exome

AF:

0.201

Gnomad FIN exome

AF:

0.224

Gnomad NFE exome

AF:

0.224

Gnomad OTH exome

AF:

0.218

GnomAD4 exome

AF:

0.212

AC:

309513

AN:

1460306

Hom.:

33687

Cov.:

AF XY:

0.212

AC XY:

154277

AN XY:

726420

show subpopulations

Gnomad4 AFR exome

AF:

0.0875

Gnomad4 AMR exome

AF:

0.143

Gnomad4 ASJ exome

AF:

0.253

Gnomad4 EAS exome

AF:

0.179

Gnomad4 SAS exome

AF:

0.203

Gnomad4 FIN exome

AF:

0.222

Gnomad4 NFE exome

AF:

0.219

Gnomad4 OTH exome

AF:

0.213

GnomAD4 genome

AF:

0.180

AC:

27418

AN:

152140

Hom.:

2765

Cov.:

AF XY:

0.182

AC XY:

13521

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.0880

Gnomad4 AMR

AF:

0.194

Gnomad4 ASJ

AF:

0.243

Gnomad4 EAS

AF:

0.173

Gnomad4 SAS

AF:

0.211

Gnomad4 FIN

AF:

0.220

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.225

Alfa

AF:

0.201

Hom.:

2513

Bravo

AF:

0.174

Asia WGS

AF:

0.182

AC:

632

AN:

3478

EpiCase

AF:

0.225

EpiControl

AF:

0.238

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 19, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Microphthalmia, isolated, with coloboma 9

Benign:1

Sep 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

5.1

DANN

Benign

0.53

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