8-125043973-G-GC
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_014846.4(WASHC5):c.2770+18_2770+19insG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 1 in 1,599,244 control chromosomes in the GnomAD database, including 799,332 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 1.0 ( 76164 hom., cov: 0)
Exomes 𝑓: 1.0 ( 723168 hom. )
Consequence
WASHC5
NM_014846.4 intron
NM_014846.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.333
Genes affected
WASHC5 (HGNC:28984): (WASH complex subunit 5) This gene encodes a 134 kDa protein named strumpellin that is predicted to have multiple transmembrane domains and a spectrin-repeat-containing domain. This ubiquitously expressed gene has its highest expression in skeletal muscle. The protein is named for Strumpell disease; a form of hereditary spastic paraplegia (HSP). Spastic paraplegias are a diverse group of disorders in which the autosomal dominant forms are characterized by progressive, lower extremity spasticity caused by axonal degeneration in the terminal portions of the longest descending and ascending corticospinal tracts. More than 30 loci (SPG1-33) have been implicated in hereditary spastic paraplegia diseases. [provided by RefSeq, Aug 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 8-125043973-G-GC is Benign according to our data. Variant chr8-125043973-G-GC is described in ClinVar as [Benign]. Clinvar id is 516650.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WASHC5 | NM_014846.4 | c.2770+18_2770+19insG | intron_variant | ENST00000318410.12 | NP_055661.3 | |||
WASHC5-AS1 | NR_170219.1 | n.97-526_97-525insC | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WASHC5 | ENST00000318410.12 | c.2770+18_2770+19insG | intron_variant | 1 | NM_014846.4 | ENSP00000318016 | P1 | |||
WASHC5-AS1 | ENST00000519140.1 | n.97-526_97-525insC | intron_variant, non_coding_transcript_variant | 4 | ||||||
WASHC5 | ENST00000517845.5 | c.2326+18_2326+19insG | intron_variant | 2 | ENSP00000429676 |
Frequencies
GnomAD3 genomes AF: 1.00 AC: 152218AN: 152226Hom.: 76105 Cov.: 0
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GnomAD3 exomes AF: 1.00 AC: 251327AN: 251344Hom.: 125655 AF XY: 1.00 AC XY: 135846AN XY: 135858
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GnomAD4 exome AF: 1.00 AC: 1446618AN: 1446900Hom.: 723168 Cov.: 29 AF XY: 1.00 AC XY: 720739AN XY: 720890
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GnomAD4 genome AF: 1.00 AC: 152336AN: 152344Hom.: 76164 Cov.: 0 AF XY: 1.00 AC XY: 74493AN XY: 74494
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Ritscher-Schinzel syndrome;C1863704:Hereditary spastic paraplegia 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 04, 2018 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at