NM_001205019.2:c.153-92A>C
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001205019.2(GK):c.153-92A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00816 in 553,588 control chromosomes in the GnomAD database, including 140 homozygotes. There are 1,155 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.026 ( 98 hom., 753 hem., cov: 24)
Exomes 𝑓: 0.0036 ( 42 hom. 402 hem. )
Consequence
GK
NM_001205019.2 intron
NM_001205019.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.339
Genes affected
GK (HGNC:4289): (glycerol kinase) The protein encoded by this gene belongs to the FGGY kinase family. This protein is a key enzyme in the regulation of glycerol uptake and metabolism. It catalyzes the phosphorylation of glycerol by ATP, yielding ADP and glycerol-3-phosphate. Mutations in this gene are associated with glycerol kinase deficiency (GKD). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant X-30667920-A-C is Benign according to our data. Variant chrX-30667920-A-C is described in ClinVar as [Benign]. Clinvar id is 1286744.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0867 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0260 AC: 2911AN: 112047Hom.: 99 Cov.: 24 AF XY: 0.0220 AC XY: 752AN XY: 34257
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GnomAD4 exome AF: 0.00364 AC: 1607AN: 441491Hom.: 42 AF XY: 0.00263 AC XY: 402AN XY: 152931
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GnomAD4 genome AF: 0.0260 AC: 2912AN: 112097Hom.: 98 Cov.: 24 AF XY: 0.0219 AC XY: 753AN XY: 34317
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 21, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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