16-92644-C-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001077350.3(NPRL3):āc.1113G>Cā(p.Pro371=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,613,668 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 Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. P371P) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPRL3 | NM_001077350.3 | c.1113G>C | p.Pro371= | synonymous_variant | 11/14 | ENST00000611875.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPRL3 | ENST00000611875.5 | c.1113G>C | p.Pro371= | synonymous_variant | 11/14 | 5 | NM_001077350.3 | P1 | |
NPRL3 | ENST00000399953.7 | c.1038G>C | p.Pro346= | synonymous_variant | 9/12 | 1 | |||
NPRL3 | ENST00000621703.4 | c.*698G>C | 3_prime_UTR_variant, NMD_transcript_variant | 8/11 | 1 | ||||
NPRL3 | ENST00000622194.4 | c.*749G>C | 3_prime_UTR_variant, NMD_transcript_variant | 9/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000443 AC: 11AN: 248370Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134880
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461412Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 726962
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74432
ClinVar
Submissions by phenotype
Epilepsy, familial focal, with variable foci 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at