1-201648912-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001389617.1(NAV1):c.1105G>A(p.Ala369Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00057 in 1,612,720 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001389617.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAV1 | NM_001389617.1 | c.1105G>A | p.Ala369Thr | missense_variant | 5/34 | ENST00000685211.1 | NP_001376546.1 | |
NAV1 | NM_001389616.1 | c.1105G>A | p.Ala369Thr | missense_variant | 4/32 | NP_001376545.1 | ||
NAV1 | NM_001389615.1 | c.1105G>A | p.Ala369Thr | missense_variant | 5/31 | NP_001376544.1 | ||
NAV1 | NM_020443.5 | c.244G>A | p.Ala82Thr | missense_variant | 1/30 | NP_065176.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAV1 | ENST00000685211.1 | c.1105G>A | p.Ala369Thr | missense_variant | 5/34 | NM_001389617.1 | ENSP00000510803 | P2 | ||
NAV1 | ENST00000367296.8 | c.244G>A | p.Ala82Thr | missense_variant | 1/30 | 5 | ENSP00000356265 | A2 | ||
NAV1 | ENST00000367302.5 | c.283G>A | p.Ala95Thr | missense_variant | 3/30 | 5 | ENSP00000356271 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00311 AC: 473AN: 152144Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000748 AC: 184AN: 245988Hom.: 3 AF XY: 0.000610 AC XY: 82AN XY: 134434
GnomAD4 exome AF: 0.000303 AC: 442AN: 1460462Hom.: 3 Cov.: 54 AF XY: 0.000267 AC XY: 194AN XY: 726548
GnomAD4 genome AF: 0.00314 AC: 478AN: 152258Hom.: 2 Cov.: 32 AF XY: 0.00293 AC XY: 218AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at