rs142099123
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM1BP4_StrongBP6_Very_StrongBS2
The NM_000170.3(GLDC):c.1331G>A(p.Cys444Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000432 in 1,613,964 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C444S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000170.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLDC | NM_000170.3 | c.1331G>A | p.Cys444Tyr | missense_variant | 10/25 | ENST00000321612.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLDC | ENST00000321612.8 | c.1331G>A | p.Cys444Tyr | missense_variant | 10/25 | 1 | NM_000170.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00238 AC: 363AN: 152236Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000589 AC: 148AN: 251450Hom.: 1 AF XY: 0.000419 AC XY: 57AN XY: 135902
GnomAD4 exome AF: 0.000229 AC: 334AN: 1461610Hom.: 2 Cov.: 31 AF XY: 0.000197 AC XY: 143AN XY: 727138
GnomAD4 genome ? AF: 0.00238 AC: 363AN: 152354Hom.: 2 Cov.: 32 AF XY: 0.00235 AC XY: 175AN XY: 74508
ClinVar
Submissions by phenotype
Non-ketotic hyperglycinemia Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 16, 2019 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 16, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 11, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at