chr17-42900921-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000151.4(G6PC1):c.45A>G(p.Ser15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S15S) has been classified as Likely benign.
Frequency
Consequence
NM_000151.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G6PC1 | NM_000151.4 | c.45A>G | p.Ser15= | synonymous_variant | 1/5 | ENST00000253801.7 | |
G6PC1 | NM_001270397.2 | c.45A>G | p.Ser15= | synonymous_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PC1 | ENST00000253801.7 | c.45A>G | p.Ser15= | synonymous_variant | 1/5 | 1 | NM_000151.4 | P1 | |
G6PC1 | ENST00000592383.5 | c.45A>G | p.Ser15= | synonymous_variant | 1/5 | 2 | |||
G6PC1 | ENST00000585489.1 | c.45A>G | p.Ser15= | synonymous_variant | 1/4 | 5 | |||
G6PC1 | ENST00000588481.1 | n.110A>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.