rs200332753
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000047.3(ARSL):c.-8_-5del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00318 in 1,192,476 control chromosomes in the GnomAD database, including 70 homozygotes. There are 986 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.016 ( 37 hom., 427 hem., cov: 20)
Exomes 𝑓: 0.0019 ( 33 hom. 559 hem. )
Consequence
ARSL
NM_000047.3 5_prime_UTR
NM_000047.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.669
Genes affected
ARSL (HGNC:719): (arylsulfatase L) Arylsulfatase E is a member of the sulfatase family. It is glycosylated postranslationally and localized to the golgi apparatus. Sulfatases are essential for the correct composition of bone and cartilage matrix. X-linked chondrodysplasia punctata, a disease characterized by abnormalities in cartilage and bone development, has been linked to mutations in this gene. Alternative splicing results in multiple transcript variants. A pseudogene related to this gene is located on the Y chromosome. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant X-2960404-GTCTC-G is Benign according to our data. Variant chrX-2960404-GTCTC-G is described in ClinVar as [Benign]. Clinvar id is 254741.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0517 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARSL | NM_000047.3 | c.-8_-5del | 5_prime_UTR_variant | 2/11 | ENST00000381134.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARSL | ENST00000381134.9 | c.-8_-5del | 5_prime_UTR_variant | 2/11 | 1 | NM_000047.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0158 AC: 1723AN: 109046Hom.: 38 Cov.: 20 AF XY: 0.0134 AC XY: 423AN XY: 31578
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GnomAD3 exomes AF: 0.00478 AC: 868AN: 181507Hom.: 16 AF XY: 0.00287 AC XY: 190AN XY: 66305
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GnomAD4 exome AF: 0.00190 AC: 2061AN: 1083390Hom.: 33 AF XY: 0.00159 AC XY: 559AN XY: 351508
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GnomAD4 genome AF: 0.0158 AC: 1728AN: 109086Hom.: 37 Cov.: 20 AF XY: 0.0135 AC XY: 427AN XY: 31628
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 08, 2018 | - - |
X-linked chondrodysplasia punctata 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 16, 2022 | - - |
Connective tissue disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Feb 10, 2022 | - - |
ARSL-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 02, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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