rs62557482
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000605275.1(GALT):n.209-151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00147 in 742,896 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000605275.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALT | ENST00000605275.1 | n.209-151C>T | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00123 AC: 187AN: 152236Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00153 AC: 905AN: 590542Hom.: 1 AF XY: 0.00153 AC XY: 479AN XY: 312904
GnomAD4 genome AF: 0.00123 AC: 187AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.00109 AC XY: 81AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: GALT c.-179C>T is located in the untranscribed region upstream of the GALT gene region. The variant allele was found at a frequency of 0.0012 in 31388 control chromosomes, predominantly at a frequency of 0.002 within the Non-Finnish European subpopulation in the gnomAD database (Genomes data). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-179C>T in individuals affected with Galactosemia and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at