rs780094
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001486(GCKR):c.1423-418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 151992 control chromosomes in the gnomAD Genomes database, including 34482 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 0.66 ( 34482 hom., cov: 32)
Consequence
GCKR
NM_001486 intron
NM_001486 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.185
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GCKR | NM_001486.4 | c.1423-418T>C | intron_variant | ENST00000264717.7 | |||
GCKR | XM_017003796.2 | c.853-418T>C | intron_variant | ||||
GCKR | XM_017003797.2 | c.853-418T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCKR | ENST00000264717.7 | c.1423-418T>C | intron_variant | 1 | NM_001486.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.664 AC: 100893AN: 151992Hom.: 34482 Cov.: 32
GnomAD3 genomes
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100893
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151992
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32
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Asia WGS
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2404
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at