rs743554
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000588479.6(GALK1):c.1108-40C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,609,576 control chromosomes in the GnomAD database, including 19,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.16 ( 2246 hom., cov: 33)
Exomes 𝑓: 0.15 ( 16899 hom. )
Consequence
GALK1
ENST00000588479.6 intron
ENST00000588479.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.441
Genes affected
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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=-0.77).
BP6
Variant 17-75758167-G-A is Benign according to our data. Variant chr17-75758167-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1180482.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALK1 | NM_000154.2 | c.1108-40C>T | intron_variant | ENST00000588479.6 | NP_000145.1 | |||
GALK1 | NM_001381985.1 | c.1108-40C>T | intron_variant | NP_001368914.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALK1 | ENST00000588479.6 | c.1108-40C>T | intron_variant | 1 | NM_000154.2 | ENSP00000465930 | P1 |
Frequencies
GnomAD3 genomes AF: 0.164 AC: 24961AN: 152070Hom.: 2241 Cov.: 33
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GnomAD3 exomes AF: 0.144 AC: 33923AN: 236046Hom.: 2712 AF XY: 0.148 AC XY: 19134AN XY: 129556
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GnomAD4 exome AF: 0.148 AC: 215599AN: 1457388Hom.: 16899 Cov.: 35 AF XY: 0.149 AC XY: 108023AN XY: 724906
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GnomAD4 genome AF: 0.164 AC: 24982AN: 152188Hom.: 2246 Cov.: 33 AF XY: 0.160 AC XY: 11906AN XY: 74396
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 29, 2018 | - - |
Deficiency of galactokinase Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 08, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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