rs78317153
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000512.5(GALNS):c.758+22C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.055 in 1,613,532 control chromosomes in the GnomAD database, including 2,915 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.050 ( 252 hom., cov: 33)
Exomes 𝑓: 0.056 ( 2663 hom. )
Consequence
GALNS
NM_000512.5 intron
NM_000512.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.66
Genes affected
GALNS (HGNC:4122): (galactosamine (N-acetyl)-6-sulfatase) This gene encodes N-acetylgalactosamine-6-sulfatase which is a lysosomal exohydrolase required for the degradation of the glycosaminoglycans, keratan sulfate, and chondroitin 6-sulfate. Sequence alterations including point, missense and nonsense mutations, as well as those that affect splicing, result in a deficiency of this enzyme. Deficiencies of this enzyme lead to Morquio A syndrome, a lysosomal storage disorder. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 16-88835703-G-A is Benign according to our data. Variant chr16-88835703-G-A is described in ClinVar as [Benign]. Clinvar id is 256336.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-88835703-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0735 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNS | NM_000512.5 | c.758+22C>T | intron_variant | ENST00000268695.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNS | ENST00000268695.10 | c.758+22C>T | intron_variant | 1 | NM_000512.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0501 AC: 7623AN: 152162Hom.: 251 Cov.: 33
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GnomAD3 exomes AF: 0.0519 AC: 13031AN: 251006Hom.: 461 AF XY: 0.0549 AC XY: 7445AN XY: 135718
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GnomAD4 exome AF: 0.0555 AC: 81165AN: 1461252Hom.: 2663 Cov.: 32 AF XY: 0.0572 AC XY: 41576AN XY: 726930
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GnomAD4 genome ? AF: 0.0501 AC: 7624AN: 152280Hom.: 252 Cov.: 33 AF XY: 0.0492 AC XY: 3662AN XY: 74460
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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:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 24, 2017 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Mucopolysaccharidosis, MPS-IV-A Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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