11-19713846-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145117.5(NAV2):c.151A>T(p.Thr51Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,613,312 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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.151A>T | p.Thr51Ser | missense_variant | 1/38 | ENST00000349880.9 | |
LEISA1 | NR_015384.2 | n.827T>A | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAV2 | ENST00000349880.9 | c.151A>T | p.Thr51Ser | missense_variant | 1/38 | 1 | NM_145117.5 | ||
NAV2 | ENST00000360655.8 | c.76-118638A>T | intron_variant | 1 | P1 | ||||
NAV2 | ENST00000396087.7 | c.151A>T | p.Thr51Ser | missense_variant | 1/41 | 5 | |||
NAV2 | ENST00000396085.6 | c.151A>T | p.Thr51Ser | missense_variant | 1/39 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000323 AC: 8AN: 247368Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134368
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461178Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 726886
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 02, 2023 | The c.151A>T (p.T51S) alteration is located in exon 1 (coding exon 1) of the NAV2 gene. This alteration results from a A to T substitution at nucleotide position 151, causing the threonine (T) at amino acid position 51 to be replaced by a serine (S). 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