rs1554089838

Variant names:

• chr5-78984789-TGGGGCGAGAAGCCGCCGGGACCCATAACTGGGTCGGCGGTCCGAGCCCCGCCTGCCAGCGCCCGCGGCCTCAAGGGCCGGGTAGGAGCGGCAGGGCGCCGGCGAAAGGCGGGGCGGGGGCGGCGCGGGCGGCGGGGGCGCCGCGTACCTGGTA-T
• rs1554089838
• NM_000046.5:c.307_312+147del

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1 PP5_Moderate

The NM_000046.5(ARSB):​c.307_312+147del​(p.Tyr103_Gln104del) variant causes a splice donor, conservative inframe deletion, splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. Y103Y) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ARSB NM_000046.5 splice_donor, conservative_inframe_deletion, splice_region, intron
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: -0.0190
• Publications: 1 publications found

Genes affected

ARSB (HGNC:714): (arylsulfatase B) Arylsulfatase B encoded by this gene belongs to the sulfatase family. The arylsulfatase B homodimer hydrolyzes sulfate groups of N-Acetyl-D-galactosamine, chondriotin sulfate, and dermatan sulfate. The protein is targeted to the lysozyme. Mucopolysaccharidosis type VI is an autosomal recessive lysosomal storage disorder resulting from a deficiency of arylsulfatase B. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Dec 2016]

ARSB Gene-Disease associations (from GenCC):

• mucopolysaccharidosis type 6

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), ClinGen, Illumina, G2P

ENSG00000308325 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease,
• PP5: Variant 5-78984789-TGGGGCGAGAAGCCGCCGGGACCCATAACTGGGTCGGCGGTCCGAGCCCCGCCTGCCAGCGCCCGCGGCCTCAAGGGCCGGGTAGGAGCGGCAGGGCGCCGGCGAAAGGCGGGGCGGGGGCGGCGCGGGCGGCGGGGGCGCCGCGTACCTGGTA-T is Pathogenic according to our data. Variant chr5-78984789-TGGGGCGAGAAGCCGCCGGGACCCATAACTGGGTCGGCGGTCCGAGCCCCGCCTGCCAGCGCCCGCGGCCTCAAGGGCCGGGTAGGAGCGGCAGGGCGCCGGCGAAAGGCGGGGCGGGGGCGGCGCGGGCGGCGGGGGCGCCGCGTACCTGGTA-T is described in ClinVar as Pathogenic. ClinVar VariationId is 559767.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000046.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARSB	NM_000046.5	MANE Select	c.307_312+147del	p.Tyr103_Gln104del	splice_donor conservative_inframe_deletion splice_region intron	Exon 1 of 8	NP_000037.2
	ARSB	NM_198709.3		c.307_312+147del	p.Tyr103_Gln104del	splice_donor conservative_inframe_deletion splice_region intron	Exon 2 of 8	NP_942002.1	P15848-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARSB	ENST00000264914.10	TSL:1 MANE Select	c.307_312+147del	p.Tyr103_Gln104del	splice_donor conservative_inframe_deletion splice_region intron	Exon 1 of 8	ENSP00000264914.4	P15848-1
	ARSB	ENST00000396151.7	TSL:1	c.307_312+147del	p.Tyr103_Gln104del	splice_donor conservative_inframe_deletion splice_region intron	Exon 2 of 8	ENSP00000379455.3	P15848-2
	ARSB	ENST00000565165.2	TSL:1	c.307_312+147del	p.Tyr103_Gln104del	splice_donor conservative_inframe_deletion splice_region intron	Exon 1 of 5	ENSP00000456339.2	A0A2U3U034

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Mucopolysaccharidosis type 6 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.019
Mutation Taster		=2/198	disease causing (ClinVar)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1554089838; hg19: chr5-78280612;