rs11063714
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000535299.5(NTF3):n.232-10798G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 152,078 control chromosomes in the GnomAD database, including 976 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 0.060 ( 976 hom., cov: 33)
Consequence
NTF3
ENST00000535299.5 intron
ENST00000535299.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0410
Publications
9 publications found
Genes affected
NTF3 (HGNC:8023): (neurotrophin 3) The protein encoded by this gene is a member of the neurotrophin family, that controls survival and differentiation of mammalian neurons. This protein is closely related to both nerve growth factor and brain-derived neurotrophic factor. It may be involved in the maintenance of the adult nervous system, and may affect development of neurons in the embryo when it is expressed in human placenta. NTF3-deficient mice generated by gene targeting display severe movement defects of the limbs. The mature peptide of this protein is identical in all mammals examined including human, pig, rat and mouse. [provided by RefSeq, Jul 2008]
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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=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NTF3 | ENST00000535299.5 | n.232-10798G>A | intron_variant | Intron 1 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0601 AC: 9128AN: 151960Hom.: 972 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
9128
AN:
151960
Hom.:
Cov.:
33
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: 0.0601 AC: 9145AN: 152078Hom.: 976 Cov.: 33 AF XY: 0.0651 AC XY: 4843AN XY: 74354 show subpopulations
GnomAD4 genome
AF:
AC:
9145
AN:
152078
Hom.:
Cov.:
33
AF XY:
AC XY:
4843
AN XY:
74354
show subpopulations
African (AFR)
AF:
AC:
3541
AN:
41440
American (AMR)
AF:
AC:
1724
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
105
AN:
3470
East Asian (EAS)
AF:
AC:
2524
AN:
5150
South Asian (SAS)
AF:
AC:
269
AN:
4802
European-Finnish (FIN)
AF:
AC:
474
AN:
10598
Middle Eastern (MID)
AF:
AC:
5
AN:
294
European-Non Finnish (NFE)
AF:
AC:
373
AN:
68002
Other (OTH)
AF:
AC:
105
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
369
739
1108
1478
1847
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
804
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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