12-76056118-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004537.7(NAP1L1):c.473A>T(p.Asp158Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000123 in 1,460,600 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D158N) has been classified as Uncertain significance.
Frequency
Consequence
NM_004537.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAP1L1 | NM_004537.7 | c.473A>T | p.Asp158Val | missense_variant | 7/15 | ENST00000618691.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAP1L1 | ENST00000618691.5 | c.473A>T | p.Asp158Val | missense_variant | 7/15 | 1 | NM_004537.7 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250176Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135244
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460600Hom.: 0 Cov.: 29 AF XY: 0.0000124 AC XY: 9AN XY: 726584
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 13, 2024 | The c.473A>T (p.D158V) alteration is located in exon 7 (coding exon 6) of the NAP1L1 gene. This alteration results from a A to T substitution at nucleotide position 473, causing the aspartic acid (D) at amino acid position 158 to be replaced by a valine (V). 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