rs560887
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021176(G6PC2):c.441-26T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152034 control chromosomes in the gnomAD Genomes database, including 49694 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 0.80 ( 49694 hom., cov: 31)
Exomes 𝑓: 0.79 ( 79660 hom. )
Consequence
G6PC2
NM_021176 intron
NM_021176 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.88
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G6PC2 | NM_021176.3 | c.441-26T>C | intron_variant | ENST00000375363.8 | |||
G6PC2 | NM_001081686.2 | c.441-930T>C | intron_variant | ||||
G6PC2 | XM_011511564.4 | c.329-930T>C | intron_variant | ||||
G6PC2 | XM_011511565.4 | c.93-26T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PC2 | ENST00000375363.8 | c.441-26T>C | intron_variant | 1 | NM_021176.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.801 AC: 121709AN: 152034Hom.: 49694 Cov.: 31
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GnomAD3 exomes AF: 0.790 AC: 198206AN: 250980Hom.: 79660 AF XY: 0.784 AC XY: 106450AN XY: 135692
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GnomAD4 exome AF: 0.748 AC: 728381AN: 974384Hom.: 276243 AF XY: 0.751 AC XY: 379924AN XY: 506166
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at