rs711634
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_182760.4(SUMF1):c.445-22T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0443 in 1,613,000 control chromosomes in the GnomAD database, including 1,875 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.032 ( 113 hom., cov: 32)
Exomes 𝑓: 0.046 ( 1762 hom. )
Consequence
SUMF1
NM_182760.4 intron
NM_182760.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.303
Genes affected
SUMF1 (HGNC:20376): (sulfatase modifying factor 1) This gene encodes an enzyme that catalyzes the hydrolysis of sulfate esters by oxidizing a cysteine residue in the substrate sulfatase to an active site 3-oxoalanine residue, which is also known as C-alpha-formylglycine. Mutations in this gene cause multiple sulfatase deficiency, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 3-4449362-A-G is Benign according to our data. Variant chr3-4449362-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 263007.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.053 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUMF1 | NM_182760.4 | c.445-22T>C | intron_variant | ENST00000272902.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUMF1 | ENST00000272902.10 | c.445-22T>C | intron_variant | 1 | NM_182760.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0323 AC: 4915AN: 152194Hom.: 113 Cov.: 32
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GnomAD3 exomes AF: 0.0313 AC: 7870AN: 251198Hom.: 188 AF XY: 0.0319 AC XY: 4327AN XY: 135790
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GnomAD4 exome AF: 0.0455 AC: 66462AN: 1460688Hom.: 1762 Cov.: 30 AF XY: 0.0443 AC XY: 32232AN XY: 726780
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GnomAD4 genome ? AF: 0.0323 AC: 4917AN: 152312Hom.: 113 Cov.: 32 AF XY: 0.0307 AC XY: 2290AN XY: 74486
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 23, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 01, 2018 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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Splicing
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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