chr11-19713892-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145117.5(NAV2):c.197T>A(p.Leu66Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,320 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAV2 | NM_145117.5 | c.197T>A | p.Leu66Gln | missense_variant | 1/38 | ENST00000349880.9 | |
LEISA1 | NR_015384.2 | n.781A>T | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAV2 | ENST00000349880.9 | c.197T>A | p.Leu66Gln | missense_variant | 1/38 | 1 | NM_145117.5 | ||
NAV2 | ENST00000360655.8 | c.76-118592T>A | intron_variant | 1 | P1 | ||||
NAV2 | ENST00000396087.7 | c.197T>A | p.Leu66Gln | missense_variant | 1/41 | 5 | |||
NAV2 | ENST00000396085.6 | c.197T>A | p.Leu66Gln | missense_variant | 1/39 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461320Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726966
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | The c.197T>A (p.L66Q) alteration is located in exon 1 (coding exon 1) of the NAV2 gene. This alteration results from a T to A substitution at nucleotide position 197, causing the leucine (L) at amino acid position 66 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at