rs140294222
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 4P and 9B. PS1_ModeratePM2BP4_StrongBP6BS1
The NM_138387.4(G6PC3):c.566G>A(p.Arg189Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000407 in 1,614,112 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_138387.4 missense
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 |
---|---|---|---|---|---|---|---|
G6PC3 | NM_138387.4 | c.566G>A | p.Arg189Gln | missense_variant | 5/6 | ENST00000269097.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PC3 | ENST00000269097.9 | c.566G>A | p.Arg189Gln | missense_variant | 5/6 | 1 | NM_138387.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000802 AC: 122AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000553 AC: 139AN: 251410Hom.: 0 AF XY: 0.000434 AC XY: 59AN XY: 135876
GnomAD4 exome AF: 0.000366 AC: 535AN: 1461888Hom.: 1 Cov.: 33 AF XY: 0.000337 AC XY: 245AN XY: 727244
GnomAD4 genome AF: 0.000801 AC: 122AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.000914 AC XY: 68AN XY: 74426
ClinVar
Submissions by phenotype
Autosomal recessive severe congenital neutropenia due to G6PC3 deficiency Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Sep 06, 2019 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at