rs12434716
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001164749.2(NPAS3):āc.1654G>Cā(p.Ala552Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,613,880 control chromosomes in the GnomAD database, including 20,956 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001164749.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPAS3 | NM_001164749.2 | c.1654G>C | p.Ala552Pro | missense_variant | 12/12 | ENST00000356141.9 | NP_001158221.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPAS3 | ENST00000356141.9 | c.1654G>C | p.Ala552Pro | missense_variant | 12/12 | 1 | NM_001164749.2 | ENSP00000348460.4 |
Frequencies
GnomAD3 genomes AF: 0.159 AC: 24147AN: 152158Hom.: 2115 Cov.: 33
GnomAD3 exomes AF: 0.138 AC: 34484AN: 250226Hom.: 2799 AF XY: 0.133 AC XY: 18057AN XY: 135524
GnomAD4 exome AF: 0.155 AC: 226648AN: 1461604Hom.: 18837 Cov.: 37 AF XY: 0.152 AC XY: 110746AN XY: 727126
GnomAD4 genome AF: 0.159 AC: 24174AN: 152276Hom.: 2119 Cov.: 33 AF XY: 0.153 AC XY: 11388AN XY: 74430
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at