14-87993123-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000153.4(GALC):c.42G>A(p.Ala14Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A14A) has been classified as Benign.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GALC
NM_000153.4 synonymous
NM_000153.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0380
Publications
15 publications found
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]
GALC Gene-Disease associations (from GenCC):
- Krabbe diseaseInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Myriad Women’s Health, Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), PanelApp Australia, ClinGen, Genomics England PanelApp
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 14-87993123-C-T is Benign according to our data. Variant chr14-87993123-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2715848.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.038 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GALC | NM_000153.4 | c.42G>A | p.Ala14Ala | synonymous_variant | Exon 1 of 17 | ENST00000261304.7 | NP_000144.2 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1434314Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 710862
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1434314
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
710862
African (AFR)
AF:
AC:
0
AN:
33048
American (AMR)
AF:
AC:
0
AN:
40836
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25674
East Asian (EAS)
AF:
AC:
0
AN:
38428
South Asian (SAS)
AF:
AC:
0
AN:
82804
European-Finnish (FIN)
AF:
AC:
0
AN:
49130
Middle Eastern (MID)
AF:
AC:
0
AN:
5678
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1099420
Other (OTH)
AF:
AC:
0
AN:
59296
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Galactosylceramide beta-galactosidase deficiency Benign:1
Jun 15, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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