14-104877962-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001112726.3(CEP170B):c.273C>T(p.Tyr91=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,605,562 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001112726.3 splice_region, 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 |
---|---|---|---|---|---|---|---|
CEP170B | NM_001112726.3 | c.273C>T | p.Tyr91= | splice_region_variant, synonymous_variant | 4/19 | ENST00000414716.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP170B | ENST00000414716.8 | c.273C>T | p.Tyr91= | splice_region_variant, synonymous_variant | 4/19 | 1 | NM_001112726.3 | P1 | |
CEP170B | ENST00000556508.5 | c.63C>T | p.Tyr21= | splice_region_variant, synonymous_variant | 3/18 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151360Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000844 AC: 2AN: 237038Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 128726
GnomAD4 exome AF: 0.0000179 AC: 26AN: 1454202Hom.: 0 Cov.: 35 AF XY: 0.0000166 AC XY: 12AN XY: 722714
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151360Hom.: 0 Cov.: 31 AF XY: 0.0000271 AC XY: 2AN XY: 73848
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | CEP170B: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at