rs886044642
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_182961.4(SYNE1):c.17203-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000556 in 1,327,034 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 Benign (★).
Frequency
Consequence
NM_182961.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNE1 | NM_182961.4 | c.17203-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000367255.10 | NP_892006.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNE1 | ENST00000367255.10 | c.17203-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_182961.4 | ENSP00000356224 | P1 | |||
SYNE1 | ENST00000423061.6 | c.16994-9C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000396024 | |||||
SYNE1 | ENST00000367256.9 | n.895-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 1 | ||||||
SYNE1 | ENST00000409694.6 | n.787-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 76AN: 135078Hom.: 0 Cov.: 25 FAILED QC
GnomAD4 exome AF: 0.000556 AC: 738AN: 1327034Hom.: 0 Cov.: 37 AF XY: 0.000596 AC XY: 394AN XY: 661006
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000563 AC: 76AN: 135104Hom.: 0 Cov.: 25 AF XY: 0.000719 AC XY: 47AN XY: 65332
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Autosomal recessive ataxia, Beauce type;C2751807:Emery-Dreifuss muscular dystrophy 4, autosomal dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 09, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at