rs199777941
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001194998.2(CEP152):c.3780G>T(p.Gly1260=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,750 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 (★). Synonymous variant affecting the same amino acid position (i.e. G1260G) has been classified as Likely benign.
Frequency
Consequence
NM_001194998.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP152 | NM_001194998.2 | c.3780G>T | p.Gly1260= | synonymous_variant | 24/27 | ENST00000380950.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP152 | ENST00000380950.7 | c.3780G>T | p.Gly1260= | synonymous_variant | 24/27 | 1 | NM_001194998.2 | A2 | |
CEP152 | ENST00000399334.7 | c.3612G>T | p.Gly1204= | synonymous_variant | 23/26 | 1 | P2 | ||
CEP152 | ENST00000325747.9 | c.3501G>T | p.Gly1167= | synonymous_variant | 23/25 | 1 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249522Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135372
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461750Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727174
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at