chr4-182622495-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080477.4(TENM3):c.750-6156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,200 control chromosomes in the GnomAD database, including 675 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 0.084 ( 675 hom., cov: 31)
Consequence
TENM3
NM_001080477.4 intron
NM_001080477.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.470
Publications
4 publications found
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 Gene-Disease associations (from GenCC):
- microphthalmia, isolated, with coloboma 9Inheritance: AR Classification: STRONG, MODERATE Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- microphthalmia, isolated, with colobomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TENM3 | NM_001080477.4 | c.750-6156G>A | intron_variant | Intron 4 of 27 | ENST00000511685.6 | NP_001073946.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0838 AC: 12745AN: 152082Hom.: 674 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
12745
AN:
152082
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0838 AC: 12751AN: 152200Hom.: 675 Cov.: 31 AF XY: 0.0882 AC XY: 6564AN XY: 74404 show subpopulations
GnomAD4 genome
AF:
AC:
12751
AN:
152200
Hom.:
Cov.:
31
AF XY:
AC XY:
6564
AN XY:
74404
show subpopulations
African (AFR)
AF:
AC:
3365
AN:
41548
American (AMR)
AF:
AC:
1825
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
415
AN:
3466
East Asian (EAS)
AF:
AC:
1184
AN:
5182
South Asian (SAS)
AF:
AC:
694
AN:
4816
European-Finnish (FIN)
AF:
AC:
1297
AN:
10580
Middle Eastern (MID)
AF:
AC:
28
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3697
AN:
68010
Other (OTH)
AF:
AC:
184
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
586
1173
1759
2346
2932
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
152
304
456
608
760
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
710
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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