10-133557856-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001143764.3(SYCE1):c.374+8C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000136 in 1,614,096 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, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYCE1 | NM_001143764.3 | c.374+8C>G | splice_region_variant, intron_variant | ENST00000343131.7 | |||
SYCE1 | NM_001143763.2 | c.374+8C>G | splice_region_variant, intron_variant | ||||
SYCE1 | NM_130784.4 | c.266+8C>G | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYCE1 | ENST00000343131.7 | c.374+8C>G | splice_region_variant, intron_variant | 1 | NM_001143764.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000223 AC: 56AN: 251454Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135908
GnomAD4 exome AF: 0.000136 AC: 199AN: 1461774Hom.: 0 Cov.: 31 AF XY: 0.000133 AC XY: 97AN XY: 727188
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74474
ClinVar
Submissions by phenotype
SYCE1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 07, 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