chr12-5494441-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001102654.2(NTF3):​c.266G>A​(p.Gly89Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 1,612,718 control chromosomes in the GnomAD database, including 4,527 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G89R) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.080 ( 1149 hom., cov: 31)
Exomes 𝑓: 0.022 ( 3378 hom. )

Consequence

NTF3
NM_001102654.2 missense

Scores

18

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.88
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.003197819).
BP6
Variant 12-5494441-G-A is Benign according to our data. Variant chr12-5494441-G-A is described in ClinVar as [Benign]. Clinvar id is 599416.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NTF3NM_001102654.2 linkuse as main transcriptc.266G>A p.Gly89Glu missense_variant 2/2 ENST00000423158.4
NTF3NM_002527.5 linkuse as main transcriptc.227G>A p.Gly76Glu missense_variant 1/1
NTF3XM_011520963.3 linkuse as main transcriptc.227G>A p.Gly76Glu missense_variant 2/2
NTF3XM_047428901.1 linkuse as main transcriptc.227G>A p.Gly76Glu missense_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NTF3ENST00000423158.4 linkuse as main transcriptc.266G>A p.Gly89Glu missense_variant 2/21 NM_001102654.2 P4P20783-2
NTF3ENST00000331010.7 linkuse as main transcriptc.227G>A p.Gly76Glu missense_variant 1/1 A1P20783-1
NTF3ENST00000543548.1 linkuse as main transcriptn.456G>A non_coding_transcript_exon_variant 2/23
NTF3ENST00000535299.5 linkuse as main transcriptn.232-12124G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0796
AC:
12087
AN:
151776
Hom.:
1139
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.193
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.182
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.159
Gnomad SAS
AF:
0.0338
Gnomad FIN
AF:
0.00755
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.00225
Gnomad OTH
AF:
0.0668
GnomAD3 exomes
AF:
0.0689
AC:
17118
AN:
248484
Hom.:
2135
AF XY:
0.0539
AC XY:
7268
AN XY:
134792
show subpopulations
Gnomad AFR exome
AF:
0.204
Gnomad AMR exome
AF:
0.281
Gnomad ASJ exome
AF:
0.00309
Gnomad EAS exome
AF:
0.149
Gnomad SAS exome
AF:
0.0249
Gnomad FIN exome
AF:
0.00875
Gnomad NFE exome
AF:
0.00206
Gnomad OTH exome
AF:
0.0430
GnomAD4 exome
AF:
0.0218
AC:
31810
AN:
1460824
Hom.:
3378
Cov.:
31
AF XY:
0.0198
AC XY:
14385
AN XY:
726784
show subpopulations
Gnomad4 AFR exome
AF:
0.201
Gnomad4 AMR exome
AF:
0.271
Gnomad4 ASJ exome
AF:
0.00283
Gnomad4 EAS exome
AF:
0.175
Gnomad4 SAS exome
AF:
0.0251
Gnomad4 FIN exome
AF:
0.00801
Gnomad4 NFE exome
AF:
0.00115
Gnomad4 OTH exome
AF:
0.0328
GnomAD4 genome
AF:
0.0799
AC:
12135
AN:
151894
Hom.:
1149
Cov.:
31
AF XY:
0.0819
AC XY:
6078
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.193
Gnomad4 AMR
AF:
0.183
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.159
Gnomad4 SAS
AF:
0.0341
Gnomad4 FIN
AF:
0.00755
Gnomad4 NFE
AF:
0.00227
Gnomad4 OTH
AF:
0.0680
Alfa
AF:
0.0192
Hom.:
491
Bravo
AF:
0.102
ESP6500AA
AF:
0.186
AC:
819
ESP6500EA
AF:
0.00314
AC:
27
ExAC
AF:
0.0613
AC:
7437
Asia WGS
AF:
0.107
AC:
371
AN:
3478
EpiCase
AF:
0.00147
EpiControl
AF:
0.00142

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Aganglionic megacolon Benign:1
Likely benign, no assertion criteria providedresearchHuman Genomics Unit, Institute for molecular medicine Finland (FIMM)-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.050
BayesDel_addAF
Benign
-0.77
T
BayesDel_noAF
Benign
-0.73
CADD
Benign
2.7
DANN
Benign
0.47
DEOGEN2
Benign
0.26
.;T
Eigen
Benign
-1.0
Eigen_PC
Benign
-0.77
FATHMM_MKL
Benign
0.049
N
LIST_S2
Benign
0.28
T;T
MetaRNN
Benign
0.0032
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-1.9
.;N
MutationTaster
Benign
1.0
P;P
PrimateAI
Benign
0.35
T
PROVEAN
Benign
0.61
N;N
REVEL
Benign
0.065
Sift
Benign
1.0
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0
.;B
Vest4
0.018
MPC
1.1
ClinPred
0.0014
T
GERP RS
4.8
Varity_R
0.029
gMVP
0.084

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs1805149; hg19: chr12-5603607; API