10-133556759-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001143764.3(SYCE1):c.528C>T(p.His176=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000252 in 1,562,448 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001143764.3 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 |
---|---|---|---|---|---|---|---|
SYCE1 | NM_001143764.3 | c.528C>T | p.His176= | splice_region_variant, synonymous_variant | 8/13 | ENST00000343131.7 | |
SYCE1 | NM_001143763.2 | c.528C>T | p.His176= | splice_region_variant, synonymous_variant | 8/13 | ||
SYCE1 | NM_130784.4 | c.420C>T | p.His140= | splice_region_variant, synonymous_variant | 8/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYCE1 | ENST00000343131.7 | c.528C>T | p.His176= | splice_region_variant, synonymous_variant | 8/13 | 1 | NM_001143764.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000207 AC: 36AN: 173912Hom.: 0 AF XY: 0.000185 AC XY: 17AN XY: 91996
GnomAD4 exome AF: 0.000264 AC: 372AN: 1410170Hom.: 0 Cov.: 31 AF XY: 0.000251 AC XY: 175AN XY: 696766
GnomAD4 genome ? AF: 0.000144 AC: 22AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74470
ClinVar
Submissions by phenotype
SYCE1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 11, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at