Variant 4-182799697-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001080477.4(TENM3):c.7446C>T(p.Gly2482=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,549,364 control chromosomes in the GnomAD database, including 13,281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2934 hom., cov: 33)

Exomes 𝑓: 0.11 ( 10347 hom. )

Consequence

TENM3
NM_001080477.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.125

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=-0.3).

BP6

Variant 4-182799697-C-T is Benign according to our data. Variant chr4-182799697-C-T is described in ClinVar as [Benign]. Clinvar id is 257355.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.125 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM3	NM_001080477.4 linkuse as main transcript	c.7446C>T	p.Gly2482=	synonymous_variant	28/28	ENST00000511685.6	NP_001073946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM3	ENST00000511685.6 linkuse as main transcript	c.7446C>T	p.Gly2482=	synonymous_variant	28/28	5	NM_001080477.4	ENSP00000424226	P1

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25608

AN:

152090

Hom.:

2913

Cov.:

show subpopulations

Gnomad AFR

AF:

0.323

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.135

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.237

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.0521

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.146

GnomAD3 exomes

AF:

0.131

AC:

19526

AN:

149450

Hom.:

1615

AF XY:

0.128

AC XY:

10249

AN XY:

80024

show subpopulations

Gnomad AFR exome

AF:

0.329

Gnomad AMR exome

AF:

0.151

Gnomad ASJ exome

AF:

0.119

Gnomad EAS exome

AF:

0.247

Gnomad SAS exome

AF:

0.119

Gnomad FIN exome

AF:

0.0531

Gnomad NFE exome

AF:

0.104

Gnomad OTH exome

AF:

0.115

GnomAD4 exome

AF:

0.113

AC:

157589

AN:

1397156

Hom.:

10347

Cov.:

AF XY:

0.112

AC XY:

77132

AN XY:

689194

show subpopulations

Gnomad4 AFR exome

AF:

0.343

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.121

Gnomad4 EAS exome

AF:

0.179

Gnomad4 SAS exome

AF:

0.124

Gnomad4 FIN exome

AF:

0.0545

Gnomad4 NFE exome

AF:

0.104

Gnomad4 OTH exome

AF:

0.124

GnomAD4 genome

AF:

0.169

AC:

25672

AN:

152208

Hom.:

2934

Cov.:

AF XY:

0.166

AC XY:

12319

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.324

Gnomad4 AMR

AF:

0.136

Gnomad4 ASJ

AF:

0.120

Gnomad4 EAS

AF:

0.237

Gnomad4 SAS

AF:

0.123

Gnomad4 FIN

AF:

0.0521

Gnomad4 NFE

AF:

0.102

Gnomad4 OTH

AF:

0.146

Alfa

AF:

0.120

Hom.:

706

Bravo

AF:

0.185

Asia WGS

AF:

0.169

AC:

588

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 22, 2018	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. -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

DANN

Benign

0.83

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