chr11-19832542-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_145117.5(NAV2):c.326G>A(p.Arg109Lys) variant causes a missense change. The variant allele was found at a frequency of 0.33 in 1,613,540 control chromosomes in the GnomAD database, including 93,706 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_145117.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAV2 | NM_145117.5 | c.326G>A | p.Arg109Lys | missense_variant | 2/38 | ENST00000349880.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAV2 | ENST00000349880.9 | c.326G>A | p.Arg109Lys | missense_variant | 2/38 | 1 | NM_145117.5 |
Frequencies
GnomAD3 genomes ? AF: 0.418 AC: 63495AN: 151806Hom.: 14962 Cov.: 32
GnomAD3 exomes AF: 0.347 AC: 87291AN: 251430Hom.: 16545 AF XY: 0.334 AC XY: 45443AN XY: 135892
GnomAD4 exome AF: 0.321 AC: 469123AN: 1461614Hom.: 78709 Cov.: 37 AF XY: 0.318 AC XY: 230912AN XY: 727120
GnomAD4 genome ? AF: 0.418 AC: 63573AN: 151926Hom.: 14997 Cov.: 32 AF XY: 0.413 AC XY: 30681AN XY: 74250
ClinVar
Submissions by phenotype
NAV2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 30, 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at