rs398076
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000153.4(GALC):c.1350C>T(p.Ser450Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 1,610,008 control chromosomes in the GnomAD database, including 126,114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000153.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALC | NM_000153.4 | c.1350C>T | p.Ser450Ser | synonymous_variant | Exon 13 of 17 | ENST00000261304.7 | NP_000144.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.396 AC: 60115AN: 151636Hom.: 12146 Cov.: 31
GnomAD3 exomes AF: 0.368 AC: 91227AN: 248096Hom.: 17396 AF XY: 0.372 AC XY: 50061AN XY: 134614
GnomAD4 exome AF: 0.392 AC: 571804AN: 1458254Hom.: 113955 Cov.: 35 AF XY: 0.393 AC XY: 284890AN XY: 725544
GnomAD4 genome AF: 0.396 AC: 60162AN: 151754Hom.: 12159 Cov.: 31 AF XY: 0.394 AC XY: 29204AN XY: 74144
ClinVar
Submissions by phenotype
Galactosylceramide beta-galactosidase deficiency Benign:5
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:4
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not provided Benign:3
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at