rs774225566
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_ModeratePM2PP3_ModeratePP5
The NM_001143764.3(SYCE1):c.197-2A>G variant causes a splice acceptor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,457,642 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_001143764.3 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYCE1 | NM_001143764.3 | c.197-2A>G | splice_acceptor_variant | ENST00000343131.7 | |||
SYCE1 | NM_001143763.2 | c.197-2A>G | splice_acceptor_variant | ||||
SYCE1 | NM_130784.4 | c.89-2A>G | splice_acceptor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYCE1 | ENST00000343131.7 | c.197-2A>G | splice_acceptor_variant | 1 | NM_001143764.3 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000812 AC: 2AN: 246392Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133298
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1457642Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 725162
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Spermatogenic failure 15 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at