chr1-201648725-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP7BS2

The NM_001389617.1(NAV1):​c.918C>T​(p.Gly306Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,414,050 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. G306G) has been classified as Benign.

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )

Consequence

NAV1
NM_001389617.1 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.839
Variant links:
Genes affected
NAV1 (HGNC:15989): (neuron navigator 1) This gene belongs to the neuron navigator family and is expressed predominantly in the nervous system. The encoded protein contains coiled-coil domains and a conserved AAA domain characteristic for ATPases associated with a variety of cellular activities. This gene is similar to unc-53, a Caenorhabditis elegans gene involved in axon guidance. The exact function of this gene is not known, but it is thought to play a role in in neuronal development and regeneration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP7
Synonymous conserved (PhyloP=0.839 with no splicing effect.
BS2
High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NAV1NM_001389617.1 linkc.918C>T p.Gly306Gly synonymous_variant Exon 5 of 34 ENST00000685211.1 NP_001376546.1
NAV1NM_001389616.1 linkc.918C>T p.Gly306Gly synonymous_variant Exon 4 of 32 NP_001376545.1
NAV1NM_001389615.1 linkc.918C>T p.Gly306Gly synonymous_variant Exon 5 of 31 NP_001376544.1
NAV1NM_020443.5 linkc.57C>T p.Gly19Gly synonymous_variant Exon 1 of 30 NP_065176.3 Q8NEY1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NAV1ENST00000685211.1 linkc.918C>T p.Gly306Gly synonymous_variant Exon 5 of 34 NM_001389617.1 ENSP00000510803.1 A0A8I5KSE4
NAV1ENST00000367296.8 linkc.57C>T p.Gly19Gly synonymous_variant Exon 1 of 30 5 ENSP00000356265.4 Q8NEY1-1
NAV1ENST00000367302.5 linkc.96C>T p.Gly32Gly synonymous_variant Exon 3 of 30 5 ENSP00000356271.1 A0A0A0MRJ3

Frequencies

GnomAD3 genomes
AF:
0.0000526
AC:
8
AN:
152014
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000193
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000555
AC:
7
AN:
1262036
Hom.:
0
Cov.:
54
AF XY:
0.00000485
AC XY:
3
AN XY:
619042
show subpopulations
Gnomad4 AFR exome
AF:
0.000156
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000168
Gnomad4 FIN exome
AF:
0.0000307
Gnomad4 NFE exome
AF:
9.80e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000526
AC:
8
AN:
152014
Hom.:
0
Cov.:
32
AF XY:
0.0000404
AC XY:
3
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.000193
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.28
CADD
Benign
14
DANN
Benign
0.97

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs571656889; hg19: chr1-201617853; API