rs161628
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001270397.2(G6PC1):c.355G>A(p.Asp119Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00421 in 1,613,148 control chromosomes in the GnomAD database, including 246 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001270397.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
G6PC1 | ENST00000253801.7 | c.432G>A | p.Pro144Pro | synonymous_variant | Exon 3 of 5 | 1 | NM_000151.4 | ENSP00000253801.1 | ||
G6PC1 | ENST00000592383.5 | c.355G>A | p.Asp119Asn | missense_variant | Exon 3 of 5 | 2 | ENSP00000465958.1 | |||
G6PC1 | ENST00000585489.1 | c.432G>A | p.Pro144Pro | synonymous_variant | Exon 3 of 4 | 5 | ENSP00000466202.1 |
Frequencies
GnomAD3 genomes AF: 0.0222 AC: 3370AN: 152130Hom.: 123 Cov.: 31
GnomAD3 exomes AF: 0.00584 AC: 1464AN: 250692Hom.: 48 AF XY: 0.00420 AC XY: 569AN XY: 135462
GnomAD4 exome AF: 0.00233 AC: 3401AN: 1460900Hom.: 120 Cov.: 30 AF XY: 0.00204 AC XY: 1482AN XY: 726756
GnomAD4 genome AF: 0.0223 AC: 3390AN: 152248Hom.: 126 Cov.: 31 AF XY: 0.0214 AC XY: 1593AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2014 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Nov 07, 2017 | Variant summary: The G6PC c.432G>A (p.Pro144Pro) variant causes a missense change located in the Phosphatidic acid phosphatase type 2/haloperoxidase domain (IPR000326) (InterPro) involving the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a polymorphism outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 2067/276430 control chromosomes in gnomAD, including 72 homozygous individuals, at a frequency of 0.0074775, which is approximately 4 times the estimated maximal expected allele frequency of a pathogenic G6PC variant (0.0017321), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign. - |
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA Benign:3
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 25, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2025 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 30, 2022 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 14, 2017 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at