Variant rs7654255 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001080477.4(TENM3):c.3579T>C(p.Tyr1193=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,613,556 control chromosomes in the GnomAD database, including 69,117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 6832 hom., cov: 33)

Exomes 𝑓: 0.29 ( 62285 hom. )

Consequence

TENM3
NM_001080477.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.552

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 4-182743369-T-C is Benign according to our data. Variant chr4-182743369-T-C is described in ClinVar as [Benign]. Clinvar id is 257350.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.552 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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.3579T>C	p.Tyr1193=	synonymous_variant	19/28	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.3579T>C	p.Tyr1193=	synonymous_variant	19/28	5	NM_001080477.4	ENSP00000424226	P1
TENM3	ENST00000502950.1 linkuse as main transcript	n.1966T>C		non_coding_transcript_exon_variant	11/15	2

Frequencies

GnomAD3 genomes

AF:

0.293

AC:

44557

AN:

151996

Hom.:

6830

Cov.:

show subpopulations

Gnomad AFR

AF:

0.347

Gnomad AMI

AF:

0.117

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.270

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.173

Gnomad FIN

AF:

0.322

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.282

GnomAD3 exomes

AF:

0.257

AC:

63948

AN:

249150

Hom.:

8968

AF XY:

0.254

AC XY:

34396

AN XY:

135160

show subpopulations

Gnomad AFR exome

AF:

0.346

Gnomad AMR exome

AF:

0.135

Gnomad ASJ exome

AF:

0.260

Gnomad EAS exome

AF:

0.153

Gnomad SAS exome

AF:

0.182

Gnomad FIN exome

AF:

0.329

Gnomad NFE exome

AF:

0.304

Gnomad OTH exome

AF:

0.263

GnomAD4 exome

AF:

0.286

AC:

418634

AN:

1461442

Hom.:

62285

Cov.:

AF XY:

0.283

AC XY:

205808

AN XY:

727016

show subpopulations

Gnomad4 AFR exome

AF:

0.344

Gnomad4 AMR exome

AF:

0.142

Gnomad4 ASJ exome

AF:

0.257

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.180

Gnomad4 FIN exome

AF:

0.326

Gnomad4 NFE exome

AF:

0.304

Gnomad4 OTH exome

AF:

0.276

GnomAD4 genome

AF:

0.293

AC:

44587

AN:

152114

Hom.:

6832

Cov.:

AF XY:

0.288

AC XY:

21415

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.347

Gnomad4 AMR

AF:

0.184

Gnomad4 ASJ

AF:

0.270

Gnomad4 EAS

AF:

0.153

Gnomad4 SAS

AF:

0.173

Gnomad4 FIN

AF:

0.322

Gnomad4 NFE

AF:

0.304

Gnomad4 OTH

AF:

0.282

Alfa

AF:

0.294

Hom.:

13436

Bravo

AF:

0.288

Asia WGS

AF:

0.205

AC:

714

AN:

3478

EpiCase

AF:

0.286

EpiControl

AF:

0.286

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 08, 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

-0.68

CADD

Benign

0.46

DANN

Benign

0.23

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