11-19713771-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_145117.5(NAV2):c.76C>T(p.His26Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000616 in 1,460,508 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAV2 | ENST00000349880.9 | c.76C>T | p.His26Tyr | missense_variant | Exon 1 of 38 | 1 | NM_145117.5 | ENSP00000309577.6 | ||
NAV2 | ENST00000360655.8 | c.76-118713C>T | intron_variant | Intron 1 of 37 | 1 | ENSP00000353871.4 | ||||
NAV2 | ENST00000396087.7 | c.76C>T | p.His26Tyr | missense_variant | Exon 1 of 41 | 5 | ENSP00000379396.3 | |||
NAV2 | ENST00000396085.6 | c.76C>T | p.His26Tyr | missense_variant | Exon 1 of 39 | 5 | ENSP00000379394.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000818 AC: 2AN: 244412Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133130
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460508Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 726536
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.76C>T (p.H26Y) alteration is located in exon 1 (coding exon 1) of the NAV2 gene. This alteration results from a C to T substitution at nucleotide position 76, causing the histidine (H) at amino acid position 26 to be replaced by a tyrosine (Y). 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