rs549291288
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001077350.3(NPRL3):c.919C>T(p.Leu307=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000674 in 1,613,510 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L307L) has been classified as Likely benign.
Frequency
Consequence
NM_001077350.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPRL3 | NM_001077350.3 | c.919C>T | p.Leu307= | synonymous_variant | 9/14 | ENST00000611875.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPRL3 | ENST00000611875.5 | c.919C>T | p.Leu307= | synonymous_variant | 9/14 | 5 | NM_001077350.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000460 AC: 70AN: 152224Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00129 AC: 320AN: 248434Hom.: 4 AF XY: 0.00172 AC XY: 232AN XY: 134824
GnomAD4 exome AF: 0.000697 AC: 1019AN: 1461168Hom.: 11 Cov.: 31 AF XY: 0.000960 AC XY: 698AN XY: 726874
GnomAD4 genome ? AF: 0.000453 AC: 69AN: 152342Hom.: 1 Cov.: 32 AF XY: 0.000644 AC XY: 48AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 22, 2020 | - - |
Epilepsy, familial focal, with variable foci 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 09, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at