chr11-19713850-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_145117.5(NAV2):c.155A>G(p.Tyr52Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00189 in 1,613,580 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_145117.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAV2 | NM_145117.5 | c.155A>G | p.Tyr52Cys | missense_variant | 1/38 | ENST00000349880.9 | |
LEISA1 | NR_015384.2 | n.823T>C | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAV2 | ENST00000349880.9 | c.155A>G | p.Tyr52Cys | missense_variant | 1/38 | 1 | NM_145117.5 | ||
NAV2 | ENST00000360655.8 | c.76-118634A>G | intron_variant | 1 | P1 | ||||
NAV2 | ENST00000396087.7 | c.155A>G | p.Tyr52Cys | missense_variant | 1/41 | 5 | |||
NAV2 | ENST00000396085.6 | c.155A>G | p.Tyr52Cys | missense_variant | 1/39 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00150 AC: 229AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00127 AC: 315AN: 247790Hom.: 0 AF XY: 0.00135 AC XY: 182AN XY: 134520
GnomAD4 exome AF: 0.00193 AC: 2821AN: 1461290Hom.: 1 Cov.: 31 AF XY: 0.00185 AC XY: 1348AN XY: 726940
GnomAD4 genome ? AF: 0.00150 AC: 229AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.00128 AC XY: 95AN XY: 74474
ClinVar
Submissions by phenotype
NAV2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 20, 2023 | This variant is classified as likely 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