2-27099768-TCA-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_006488.3(KHK):c.*24_*25delAC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 1,612,704 control chromosomes in the GnomAD database, including 409 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.014 ( 28 hom., cov: 32)
Exomes 𝑓: 0.020 ( 381 hom. )
Consequence
KHK
NM_006488.3 3_prime_UTR
NM_006488.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.312
Genes affected
KHK (HGNC:6315): (ketohexokinase) This gene encodes ketohexokinase that catalyzes conversion of fructose to fructose-1-phosphate. The product of this gene is the first enzyme with a specialized pathway that catabolizes dietary fructose. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
CGREF1 (HGNC:16962): (cell growth regulator with EF-hand domain 1) Predicted to enable calcium ion binding activity. Predicted to be involved in negative regulation of cell population proliferation. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 2-27099768-TCA-T is Benign according to our data. Variant chr2-27099768-TCA-T is described in ClinVar as [Likely_benign]. Clinvar id is 335500.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0138 (2096/152254) while in subpopulation SAS AF= 0.0411 (198/4822). AF 95% confidence interval is 0.0364. There are 28 homozygotes in gnomad4. There are 1020 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 28 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0138 AC: 2095AN: 152136Hom.: 28 Cov.: 32
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GnomAD3 exomes AF: 0.0185 AC: 4531AN: 244720Hom.: 52 AF XY: 0.0208 AC XY: 2766AN XY: 132700
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GnomAD4 exome AF: 0.0195 AC: 28490AN: 1460450Hom.: 381 AF XY: 0.0204 AC XY: 14846AN XY: 726400
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GnomAD4 genome AF: 0.0138 AC: 2096AN: 152254Hom.: 28 Cov.: 32 AF XY: 0.0137 AC XY: 1020AN XY: 74444
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Essential fructosuria Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at