GeneBe

NM_145117.5:c.39A>G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_145117.5(NAV2):​c.39A>G​(p.Gly13Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000693 in 1,443,134 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G13G) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

NAV2
NM_145117.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.53

Publications

1 publications found
Variant links:
Genes affected
NAV2 (HGNC:15997): (neuron navigator 2) This gene encodes a member of the neuron navigator gene family, which may play a role in cellular growth and migration. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
LEISA1 (HGNC:55264): (lncRNA enhancing IL-6/STAT3 signaling activation 1)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP7
Synonymous conserved (PhyloP=2.53 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NAV2NM_145117.5 linkc.39A>G p.Gly13Gly synonymous_variant Exon 1 of 38 ENST00000349880.9 NP_660093.2 Q8IVL1-3A7E2D6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NAV2ENST00000349880.9 linkc.39A>G p.Gly13Gly synonymous_variant Exon 1 of 38 1 NM_145117.5 ENSP00000309577.6 Q8IVL1-3
NAV2ENST00000360655.8 linkc.76-118750A>G intron_variant Intron 1 of 37 1 ENSP00000353871.4 Q8IVL1-4
NAV2ENST00000396087.7 linkc.39A>G p.Gly13Gly synonymous_variant Exon 1 of 41 5 ENSP00000379396.3 Q8IVL1-1
NAV2ENST00000396085.6 linkc.39A>G p.Gly13Gly synonymous_variant Exon 1 of 39 5 ENSP00000379394.1 Q8IVL1-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.93e-7
AC:
1
AN:
1443134
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
714842
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
32938
American (AMR)
AF:
0.00
AC:
0
AN:
43318
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25604
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39174
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85134
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
52440
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5398
European-Non Finnish (NFE)
AF:
9.09e-7
AC:
1
AN:
1099740
Other (OTH)
AF:
0.00
AC:
0
AN:
59388
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
1
EpiCase
AF:
0.0000547
EpiControl
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
12
DANN
Benign
0.70
PhyloP100
2.5
PromoterAI
0.0036
Neutral

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

Other links and lift over

dbSNP: rs146393896; hg19: chr11-19735280; API