chr11-19880000-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145117.5(NAV2):c.643G>A(p.Gly215Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000083 in 1,613,540 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_145117.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAV2 | NM_145117.5 | c.643G>A | p.Gly215Arg | missense_variant | 5/38 | ENST00000349880.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAV2 | ENST00000349880.9 | c.643G>A | p.Gly215Arg | missense_variant | 5/38 | 1 | NM_145117.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000180 AC: 45AN: 249610Hom.: 0 AF XY: 0.000222 AC XY: 30AN XY: 135056
GnomAD4 exome AF: 0.0000883 AC: 129AN: 1461474Hom.: 1 Cov.: 31 AF XY: 0.000128 AC XY: 93AN XY: 727044
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.643G>A (p.G215R) alteration is located in exon 5 (coding exon 5) of the NAV2 gene. This alteration results from a G to A substitution at nucleotide position 643, causing the glycine (G) at amino acid position 215 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 13, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at