X-2960404-GTCTC-GTCTCTC
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_000047.3(ARSL):c.-5_-4insGA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000923 in 1,083,425 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 20)
Exomes 𝑓: 9.2e-7 ( 0 hom. 1 hem. )
Consequence
ARSL
NM_000047.3 5_prime_UTR
NM_000047.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.26
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant X-2960404-G-GTC is Benign according to our data. Variant chrX-2960404-G-GTC is described in ClinVar as [Benign]. Clinvar id is 1686515.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARSL | NM_000047.3 | c.-5_-4insGA | 5_prime_UTR_variant | 2/11 | ENST00000381134.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARSL | ENST00000381134.9 | c.-5_-4insGA | 5_prime_UTR_variant | 2/11 | 1 | NM_000047.3 | P4 |
Frequencies
GnomAD3 genomes Cov.: 20
GnomAD3 genomes
Cov.:
20
GnomAD4 exome AF: 9.23e-7 AC: 1AN: 1083425Hom.: 0 Cov.: 28 AF XY: 0.00000284 AC XY: 1AN XY: 351497
GnomAD4 exome
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1083425
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28
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1
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351497
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GnomAD4 genome Cov.: 20
GnomAD4 genome
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20
Bravo
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at