chr9-6556229-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000170.3(GLDC):āc.2126A>Gā(p.Asn709Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000471 in 1,612,448 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000170.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLDC | NM_000170.3 | c.2126A>G | p.Asn709Ser | missense_variant | 18/25 | ENST00000321612.8 | NP_000161.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLDC | ENST00000321612.8 | c.2126A>G | p.Asn709Ser | missense_variant | 18/25 | 1 | NM_000170.3 | ENSP00000370737.4 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251452Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135892
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1460230Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 726580
GnomAD4 genome AF: 0.000243 AC: 37AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74364
ClinVar
Submissions by phenotype
Glycine encephalopathy Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2022 | The c.2126A>G (p.N709S) alteration is located in exon 18 (coding exon 18) of the GLDC gene. This alteration results from a A to G substitution at nucleotide position 2126, causing the asparagine (N) at amino acid position 709 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 18, 2024 | In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 32421718) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at