chr14-104724461-AGGTGCGGGCTGGGGCGCCG-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The ENST00000330877.7(ADSS1):c.192_192+18delGGTGCGGGCTGGGGCGCCG(p.Gly66HisfsTer52) variant causes a frameshift, splice donor, splice region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000016 in 1,247,256 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
ENST00000330877.7 frameshift, splice_donor, splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADSS1 | NM_152328.5 | c.192+3_192+21delGCGGGCTGGGGCGCCGGGT | splice_region_variant, intron_variant | Intron 1 of 12 | ENST00000330877.7 | NP_689541.1 | ||
ADSS1 | XM_006720026.4 | c.192+3_192+21delGCGGGCTGGGGCGCCGGGT | splice_region_variant, intron_variant | Intron 1 of 13 | XP_006720089.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADSS1 | ENST00000330877.7 | c.192_192+18delGGTGCGGGCTGGGGCGCCG | p.Gly66HisfsTer52 | frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant | Exon 1 of 13 | 1 | NM_152328.5 | ENSP00000331260.2 | ||
ADSS1 | ENST00000710323.1 | c.192_192+18delGGTGCGGGCTGGGGCGCCG | p.Gly66HisfsTer52 | frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant | Exon 1 of 13 | ENSP00000518203.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151894Hom.: 0 Cov.: 33
GnomAD4 exome AF: 9.13e-7 AC: 1AN: 1095362Hom.: 0 AF XY: 0.00000193 AC XY: 1AN XY: 518228
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151894Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74190
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 04, 2024 | Variant summary: ADSS1 c.-5428_-5410del19 is located in the untranscribed region upstream of the ADSS1 gene region (NM_199165). However, this variant can be interpreted as c.192+3_192+21del in NM_152328. Computational tools predict this variant may impact the splicing of NM_152328 transcript: two predict that this variant abolishes a 5' splice donor site and two predict that this variant weakens a 5' splice donor site. The variant was absent in 31260 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-5428_-5410del19 in individuals affected with Myopathy, Distal, 5 and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined aboe, the variant was classified as uncertain significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at