Variant rs13340295 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001080477.4(TENM3):c.2369-18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0584 in 1,605,396 control chromosomes in the GnomAD database, including 3,474 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.081 ( 779 hom., cov: 32)

Exomes 𝑓: 0.056 ( 2695 hom. )

Consequence

TENM3
NM_001080477.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.00600

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:

TENM3 (HGNC:):

TENM3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 4-182728947-G-A is Benign according to our data. Variant chr4-182728947-G-A is described in ClinVar as [Benign]. Clinvar id is 257348.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 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.2369-18G>A		intron_variant		ENST00000511685.6	NP_001073946.1	Q9P273A0A140VJW8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENM3	ENST00000511685.6 linkuse as main transcript	c.2369-18G>A		intron_variant		5	NM_001080477.4	ENSP00000424226.1		Q9P273
TENM3	ENST00000502950.1 linkuse as main transcript	n.756-18G>A		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0813

AC:

12347

AN:

151794

Hom.:

774

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.0565

Gnomad ASJ

AF:

0.0444

Gnomad EAS

AF:

0.000579

Gnomad SAS

AF:

0.0418

Gnomad FIN

AF:

0.0140

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0562

Gnomad OTH

AF:

0.0755

GnomAD3 exomes

AF:

0.0523

AC:

12883

AN:

246326

Hom.:

524

AF XY:

0.0515

AC XY:

6882

AN XY:

133584

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.0380

Gnomad ASJ exome

AF:

0.0452

Gnomad EAS exome

AF:

0.0000560

Gnomad SAS exome

AF:

0.0448

Gnomad FIN exome

AF:

0.0159

Gnomad NFE exome

AF:

0.0577

Gnomad OTH exome

AF:

0.0573

GnomAD4 exome

AF:

0.0560

AC:

81338

AN:

1453492

Hom.:

2695

Cov.:

AF XY:

0.0553

AC XY:

39975

AN XY:

723070

show subpopulations

Gnomad4 AFR exome

AF:

0.169

Gnomad4 AMR exome

AF:

0.0398

Gnomad4 ASJ exome

AF:

0.0447

Gnomad4 EAS exome

AF:

0.000152

Gnomad4 SAS exome

AF:

0.0469

Gnomad4 FIN exome

AF:

0.0173

Gnomad4 NFE exome

AF:

0.0575

Gnomad4 OTH exome

AF:

0.0624

GnomAD4 genome

AF:

0.0814

AC:

12361

AN:

151904

Hom.:

779

Cov.:

AF XY:

0.0789

AC XY:

5856

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.168

Gnomad4 AMR

AF:

0.0564

Gnomad4 ASJ

AF:

0.0444

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.0410

Gnomad4 FIN

AF:

0.0140

Gnomad4 NFE

AF:

0.0562

Gnomad4 OTH

AF:

0.0747

Alfa

AF:

0.0655

Hom.:

374

Bravo

AF:

0.0890

Asia WGS

AF:

0.0340

AC:

118

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	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	Dec 01, 2018	- -

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

-0.87

CADD

Benign

0.66

DANN

Benign

0.26

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