chr16-88835869-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000512.5(GALNS):c.634-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 1,613,416 control chromosomes in the GnomAD database, including 7,807 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_000512.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0905 AC: 13769AN: 152178Hom.: 692 Cov.: 33
GnomAD3 exomes AF: 0.0981 AC: 24607AN: 250874Hom.: 1414 AF XY: 0.103 AC XY: 13911AN XY: 135676
GnomAD4 exome AF: 0.0938 AC: 137095AN: 1461120Hom.: 7112 Cov.: 35 AF XY: 0.0966 AC XY: 70207AN XY: 726854
GnomAD4 genome AF: 0.0905 AC: 13787AN: 152296Hom.: 695 Cov.: 33 AF XY: 0.0901 AC XY: 6708AN XY: 74478
ClinVar
Submissions by phenotype
not specified Benign:4
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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. -
Variant summary: GALNS c.634-20C>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. The variant allele was found at a frequency of 0.096 in 276718 control chromosomes in the gnomAD database, including 1472 homozygotes. The observed variant frequency is approximately 47-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in GALNS causing Mucopolysaccharidosis Type IVA (Morquio Syndrome A) phenotype (0.002), strongly suggesting that the variant is benign. Four ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as benign. Based on the evidence outlined above, the variant was classified as benign. -
Mucopolysaccharidosis, MPS-IV-A Benign:4
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at