rs11063714

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0410

Publications

9 publications found
Variant links:
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]

Genome browser will be placed here

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
NTF3ENST00000535299.5 linkn.232-10798G>A intron_variant Intron 1 of 4 5

Frequencies

GnomAD3 genomes
AF:
0.0601
AC:
9128
AN:
151960
Hom.:
972
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0851
Gnomad AMI
AF:
0.0274
Gnomad AMR
AF:
0.113
Gnomad ASJ
AF:
0.0303
Gnomad EAS
AF:
0.490
Gnomad SAS
AF:
0.0566
Gnomad FIN
AF:
0.0447
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00548
Gnomad OTH
AF:
0.0507
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0601
AC:
9145
AN:
152078
Hom.:
976
Cov.:
33
AF XY:
0.0651
AC XY:
4843
AN XY:
74354
show subpopulations
African (AFR)
AF:
0.0854
AC:
3541
AN:
41440
American (AMR)
AF:
0.113
AC:
1724
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.0303
AC:
105
AN:
3470
East Asian (EAS)
AF:
0.490
AC:
2524
AN:
5150
South Asian (SAS)
AF:
0.0560
AC:
269
AN:
4802
European-Finnish (FIN)
AF:
0.0447
AC:
474
AN:
10598
Middle Eastern (MID)
AF:
0.0170
AC:
5
AN:
294
European-Non Finnish (NFE)
AF:
0.00549
AC:
373
AN:
68002
Other (OTH)
AF:
0.0497
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
88
176
264
352
440
<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:
0.0314
Hom.:
1199
Bravo
AF:
0.0722
Asia WGS
AF:
0.232
AC:
804
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
6.2
DANN
Benign
0.48
PhyloP100
0.041

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs11063714; hg19: chr12-5604933; API