chr11-19713865-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_145117.5(NAV2):c.170C>G(p.Pro57Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000967 in 1,613,716 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0053 ( 11 hom., cov: 33)
Exomes 𝑓: 0.00051 ( 11 hom. )
Consequence
NAV2
NM_145117.5 missense
NM_145117.5 missense
Scores
8
9
Clinical Significance
Conservation
PhyloP100: 4.90
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]
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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=0.0059349537).
BP6
?
Variant 11-19713865-C-G is Benign according to our data. Variant chr11-19713865-C-G is described in ClinVar as [Benign]. Clinvar id is 3040987.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00531 (809/152344) while in subpopulation AFR AF= 0.0185 (771/41580). AF 95% confidence interval is 0.0175. There are 11 homozygotes in gnomad4. There are 402 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 11 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAV2 | NM_145117.5 | c.170C>G | p.Pro57Arg | missense_variant | 1/38 | ENST00000349880.9 | |
LEISA1 | NR_015384.2 | n.808G>C | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAV2 | ENST00000349880.9 | c.170C>G | p.Pro57Arg | missense_variant | 1/38 | 1 | NM_145117.5 | ||
NAV2 | ENST00000360655.8 | c.76-118619C>G | intron_variant | 1 | P1 | ||||
NAV2 | ENST00000396087.7 | c.170C>G | p.Pro57Arg | missense_variant | 1/41 | 5 | |||
NAV2 | ENST00000396085.6 | c.170C>G | p.Pro57Arg | missense_variant | 1/39 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00533 AC: 811AN: 152226Hom.: 11 Cov.: 33
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GnomAD3 exomes AF: 0.00143 AC: 356AN: 248544Hom.: 4 AF XY: 0.00101 AC XY: 136AN XY: 134830
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GnomAD4 exome AF: 0.000514 AC: 751AN: 1461372Hom.: 11 Cov.: 31 AF XY: 0.000411 AC XY: 299AN XY: 727002
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
NAV2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 25, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.;N;N
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;.;N;N
REVEL
Benign
Sift
Uncertain
D;.;.;D;D
Sift4G
Uncertain
D;D;D;D;D
Polyphen
0.94
.;.;.;P;.
Vest4
MVP
MPC
0.31
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at