5-32710680-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001363652.2(NPR3):c.18G>A(p.Leu6Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000584 in 1,540,660 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001363652.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPR3 | NM_001363652.2 | c.18G>A | p.Leu6Leu | synonymous_variant | Exon 1 of 8 | NP_001350581.1 | ||
NPR3 | NM_001204376.2 | c.18G>A | p.Leu6Leu | synonymous_variant | Exon 1 of 8 | NP_001191305.1 | ||
NPR3 | NM_001364460.2 | c.18G>A | p.Leu6Leu | synonymous_variant | Exon 1 of 7 | NP_001351389.1 | ||
NPR3 | NM_001364458.2 | c.50-14018G>A | intron_variant | Intron 1 of 7 | NP_001351387.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPR3 | ENST00000506712.1 | n.27G>A | non_coding_transcript_exon_variant | Exon 1 of 6 | 1 | |||||
NPR3 | ENST00000434067.6 | c.18G>A | p.Leu6Leu | synonymous_variant | Exon 1 of 8 | 5 | ENSP00000388408.2 | |||
NPR3 | ENST00000326958.5 | c.18G>A | p.Leu6Leu | synonymous_variant | Exon 1 of 8 | 2 | ENSP00000318340.2 | |||
NPR3 | ENST00000509104.5 | c.101-14018G>A | intron_variant | Intron 1 of 5 | 2 | ENSP00000425325.1 |
Frequencies
GnomAD3 genomes AF: 0.000361 AC: 55AN: 152176Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00163 AC: 225AN: 137864Hom.: 4 AF XY: 0.00219 AC XY: 163AN XY: 74444
GnomAD4 exome AF: 0.000608 AC: 844AN: 1388366Hom.: 11 Cov.: 31 AF XY: 0.000886 AC XY: 606AN XY: 684256
GnomAD4 genome AF: 0.000361 AC: 55AN: 152294Hom.: 1 Cov.: 32 AF XY: 0.000551 AC XY: 41AN XY: 74456
ClinVar
Submissions by phenotype
NPR3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at