19-47021166-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_002517.4(NPAS1):c.119C>A(p.Pro40Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000038 in 1,577,408 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_002517.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPAS1 | ENST00000602212.6 | c.119C>A | p.Pro40Gln | missense_variant | Exon 2 of 12 | 1 | NM_002517.4 | ENSP00000469142.1 | ||
NPAS1 | ENST00000449844.6 | c.119C>A | p.Pro40Gln | missense_variant | Exon 1 of 11 | 1 | ENSP00000405290.1 | |||
NPAS1 | ENST00000602189.5 | c.-171+1169C>A | intron_variant | Intron 1 of 9 | 5 | ENSP00000472679.1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151626Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000261 AC: 5AN: 191600Hom.: 0 AF XY: 0.0000189 AC XY: 2AN XY: 105936
GnomAD4 exome AF: 0.00000210 AC: 3AN: 1425782Hom.: 0 Cov.: 32 AF XY: 0.00000141 AC XY: 1AN XY: 707302
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151626Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74026
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.119C>A (p.P40Q) alteration is located in exon 1 (coding exon 1) of the NPAS1 gene. This alteration results from a C to A substitution at nucleotide position 119, causing the proline (P) at amino acid position 40 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