14-87950724-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000153.4(GALC):c.1186C>A(p.Arg396=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,453,926 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R396R) has been classified as Likely benign.
Frequency
Consequence
NM_000153.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALC | NM_000153.4 | c.1186C>A | p.Arg396= | synonymous_variant | 11/17 | ENST00000261304.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALC | ENST00000261304.7 | c.1186C>A | p.Arg396= | synonymous_variant | 11/17 | 1 | NM_000153.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 145132Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248096Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134674
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1453926Hom.: 0 Cov.: 28 AF XY: 0.00000276 AC XY: 2AN XY: 723630
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 145132Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 70234
ClinVar
Submissions by phenotype
Galactosylceramide beta-galactosidase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at