rs201579340
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000512.5(GALNS):c.633+22T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000842 in 1,609,932 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00068 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00086 ( 18 hom. )
Consequence
GALNS
NM_000512.5 intron
NM_000512.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.293
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 16-88836179-A-G is Benign according to our data. Variant chr16-88836179-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 256334.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNS | NM_000512.5 | c.633+22T>C | intron_variant | ENST00000268695.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNS | ENST00000268695.10 | c.633+22T>C | intron_variant | 1 | NM_000512.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000677 AC: 103AN: 152164Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00143 AC: 358AN: 249804Hom.: 11 AF XY: 0.00195 AC XY: 263AN XY: 135158
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GnomAD4 exome AF: 0.000860 AC: 1253AN: 1457650Hom.: 18 Cov.: 31 AF XY: 0.00113 AC XY: 817AN XY: 725394
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GnomAD4 genome ? AF: 0.000676 AC: 103AN: 152282Hom.: 2 Cov.: 33 AF XY: 0.000819 AC XY: 61AN XY: 74470
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | May 31, 2017 | - - |
Computational scores
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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