rs2289511
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000153.4(GALC):c.196-43C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 1,354,320 control chromosomes in the GnomAD database, including 243,647 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.59 ( 26971 hom., cov: 32)
Exomes 𝑓: 0.60 ( 216676 hom. )
Consequence
GALC
NM_000153.4 intron
NM_000153.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.658
Genes affected
GALC (HGNC:4115): (galactosylceramidase) This gene encodes a lysosomal protein which hydrolyzes the galactose ester bonds of galactosylceramide, galactosylsphingosine, lactosylceramide, and monogalactosyldiglyceride. Mutations in this gene have been associated with Krabbe disease, also known as globoid cell leukodystrophy. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [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=-0.93).
BP6
?
Variant 14-87988566-G-A is Benign according to our data. Variant chr14-87988566-G-A is described in ClinVar as [Benign]. Clinvar id is 255374.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALC | NM_000153.4 | c.196-43C>T | intron_variant | ENST00000261304.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALC | ENST00000261304.7 | c.196-43C>T | intron_variant | 1 | NM_000153.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.594 AC: 90205AN: 151872Hom.: 26963 Cov.: 32
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GnomAD3 exomes AF: 0.622 AC: 152872AN: 245826Hom.: 48168 AF XY: 0.617 AC XY: 82574AN XY: 133826
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GnomAD4 exome AF: 0.599 AC: 719780AN: 1202330Hom.: 216676 Cov.: 18 AF XY: 0.598 AC XY: 366070AN XY: 611976
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GnomAD4 genome ? AF: 0.594 AC: 90249AN: 151990Hom.: 26971 Cov.: 32 AF XY: 0.596 AC XY: 44246AN XY: 74294
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Galactosylceramide beta-galactosidase deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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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