rs201156392
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000378842.8(GALT):c.83-46G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000448 in 1,613,520 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00028 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00047 ( 5 hom. )
Consequence
GALT
ENST00000378842.8 intron
ENST00000378842.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.537
Genes affected
GALT (HGNC:4135): (galactose-1-phosphate uridylyltransferase) Galactose-1-phosphate uridyl transferase (GALT) catalyzes the second step of the Leloir pathway of galactose metabolism, namely the conversion of UDP-glucose + galactose-1-phosphate to glucose-1-phosphate + UDP-galactose. The absence of this enzyme results in classic galactosemia in humans and can be fatal in the newborn period if lactose is not removed from the diet. The pathophysiology of galactosemia has not been clearly defined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000276 (42/152360) while in subpopulation SAS AF= 0.00808 (39/4826). AF 95% confidence interval is 0.00608. There are 0 homozygotes in gnomad4. There are 32 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALT | NM_000155.4 | c.83-46G>A | intron_variant | ENST00000378842.8 | NP_000146.2 | |||
GALT | NM_001258332.2 | c.-120-46G>A | intron_variant | NP_001245261.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALT | ENST00000378842.8 | c.83-46G>A | intron_variant | 1 | NM_000155.4 | ENSP00000368119 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152242Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00104 AC: 261AN: 250662Hom.: 3 AF XY: 0.00142 AC XY: 193AN XY: 135584
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GnomAD4 exome AF: 0.000466 AC: 681AN: 1461160Hom.: 5 Cov.: 31 AF XY: 0.000678 AC XY: 493AN XY: 726884
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GnomAD4 genome AF: 0.000276 AC: 42AN: 152360Hom.: 0 Cov.: 32 AF XY: 0.000429 AC XY: 32AN XY: 74508
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at