rs79020892
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_130811.4(SNAP25):c.553-4C>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 0.00326 in 1,613,448 control chromosomes in the GnomAD database, including 132 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_130811.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNAP25 | NM_130811.4 | c.553-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000254976.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNAP25 | ENST00000254976.7 | c.553-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_130811.4 | P5 | |||
SNAP25-AS1 | ENST00000421143.6 | n.5+62590G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0165 AC: 2511AN: 151952Hom.: 77 Cov.: 30
GnomAD3 exomes AF: 0.00426 AC: 1069AN: 251166Hom.: 24 AF XY: 0.00345 AC XY: 468AN XY: 135736
GnomAD4 exome AF: 0.00187 AC: 2735AN: 1461378Hom.: 55 Cov.: 30 AF XY: 0.00165 AC XY: 1200AN XY: 726978
GnomAD4 genome ? AF: 0.0166 AC: 2518AN: 152070Hom.: 77 Cov.: 30 AF XY: 0.0169 AC XY: 1253AN XY: 74344
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 20, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 02, 2021 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 02, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Congenital myasthenic syndrome 18 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at