rs587783181
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000047.3(ARSL):c.867G>A(p.Gly289=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000331 in 1,208,031 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0000090 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.0000027 ( 0 hom. 0 hem. )
Consequence
ARSL
NM_000047.3 synonymous
NM_000047.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.03
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant X-2946122-C-T is Benign according to our data. Variant chrX-2946122-C-T is described in ClinVar as [Benign]. Clinvar id is 157738.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.03 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARSL | NM_000047.3 | c.867G>A | p.Gly289= | synonymous_variant | 7/11 | ENST00000381134.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARSL | ENST00000381134.9 | c.867G>A | p.Gly289= | synonymous_variant | 7/11 | 1 | NM_000047.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000904 AC: 1AN: 110578Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32818
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GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183253Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67709
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GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097453Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 362817
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GnomAD4 genome ? AF: 0.00000904 AC: 1AN: 110578Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32818
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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 | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at