rs79464415
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_014846.4(WASHC5):āc.867A>Cā(p.Val289Val) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000898 in 1,556,028 control chromosomes in the GnomAD database, including 11 homozygotes. 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 Likely benign (ā ā ).
Frequency
Consequence
NM_014846.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WASHC5 | NM_014846.4 | c.867A>C | p.Val289Val | splice_region_variant, synonymous_variant | 8/29 | ENST00000318410.12 | NP_055661.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WASHC5 | ENST00000318410.12 | c.867A>C | p.Val289Val | splice_region_variant, synonymous_variant | 8/29 | 1 | NM_014846.4 | ENSP00000318016.7 | ||
WASHC5 | ENST00000517845.5 | c.423A>C | p.Val141Val | splice_region_variant, synonymous_variant | 6/27 | 2 | ENSP00000429676.1 | |||
WASHC5 | ENST00000523297.5 | c.423A>C | p.Val141Val | splice_region_variant, synonymous_variant | 7/7 | 3 | ENSP00000427946.1 |
Frequencies
GnomAD3 genomes AF: 0.00451 AC: 686AN: 152166Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00122 AC: 305AN: 251020Hom.: 4 AF XY: 0.000825 AC XY: 112AN XY: 135682
GnomAD4 exome AF: 0.000507 AC: 712AN: 1403744Hom.: 5 Cov.: 24 AF XY: 0.000443 AC XY: 311AN XY: 701790
GnomAD4 genome AF: 0.00450 AC: 686AN: 152284Hom.: 6 Cov.: 32 AF XY: 0.00398 AC XY: 296AN XY: 74462
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 19, 2017 | - - |
Hereditary spastic paraplegia 8;C4551776:Ritscher-Schinzel syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 13, 2021 | - - |
Ritscher-Schinzel syndrome;C1863704:Hereditary spastic paraplegia 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at