3-33014229-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000404.4(GLB1):āc.1561T>Cā(p.Cys521Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.987 in 1,614,086 control chromosomes in the GnomAD database, including 788,793 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_000404.4 missense
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: 0.937 AC: 142425AN: 152080Hom.: 67394 Cov.: 30
GnomAD3 exomes AF: 0.983 AC: 243454AN: 247642Hom.: 120002 AF XY: 0.987 AC XY: 132858AN XY: 134558
GnomAD4 exome AF: 0.993 AC: 1451358AN: 1461888Hom.: 721355 Cov.: 92 AF XY: 0.994 AC XY: 722658AN XY: 727244
GnomAD4 genome AF: 0.936 AC: 142526AN: 152198Hom.: 67438 Cov.: 30 AF XY: 0.938 AC XY: 69839AN XY: 74424
ClinVar
Submissions by phenotype
not specified Benign:4
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not provided Benign:2Other:1
Variant interpreted as Benign and reported on 08-10-2017 by Lab or GTR ID 239772. GenomeConnect-GM1 assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. -
This variant is associated with the following publications: (PMID: 15714521, 10338095, 17664528, 20981092, 27884173) -
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Mucopolysaccharidosis, MPS-IV-B Benign:2
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Infantile GM1 gangliosidosis Benign:2
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GM1 gangliosidosis type 3 Benign:1
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GM1 gangliosidosis;C0086652:Mucopolysaccharidosis, MPS-IV-B Benign:1
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GM1 gangliosidosis type 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at