rs189675715
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_016122.3(CEP83):c.1203C>T(p.Leu401=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000617 in 1,612,756 control chromosomes in the GnomAD database, including 4 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. L401L) has been classified as Likely benign.
Frequency
Consequence
NM_016122.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP83 | NM_016122.3 | c.1203C>T | p.Leu401= | synonymous_variant | 11/17 | ENST00000397809.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP83 | ENST00000397809.10 | c.1203C>T | p.Leu401= | synonymous_variant | 11/17 | 1 | NM_016122.3 | P1 | |
CEP83 | ENST00000339839.9 | c.1203C>T | p.Leu401= | synonymous_variant | 10/16 | 1 | P1 | ||
CEP83 | ENST00000547232.5 | c.1104C>T | p.Leu368= | synonymous_variant, NMD_transcript_variant | 11/17 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00224 AC: 341AN: 151944Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000612 AC: 152AN: 248496Hom.: 0 AF XY: 0.000415 AC XY: 56AN XY: 134798
GnomAD4 exome AF: 0.000446 AC: 652AN: 1460694Hom.: 2 Cov.: 30 AF XY: 0.000410 AC XY: 298AN XY: 726628
GnomAD4 genome ? AF: 0.00226 AC: 343AN: 152062Hom.: 2 Cov.: 32 AF XY: 0.00221 AC XY: 164AN XY: 74318
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | CEP83: BP4, BP7 - |
Nephronophthisis 18 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at