rs184463452
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_ModerateBP6_Very_Strong
The NM_000170.3(GLDC):c.1581-5C>T variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.000099 in 1,606,774 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000170.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLDC | NM_000170.3 | c.1581-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000321612.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLDC | ENST00000321612.8 | c.1581-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000170.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000370 AC: 93AN: 251120Hom.: 1 AF XY: 0.000339 AC XY: 46AN XY: 135750
GnomAD4 exome AF: 0.0000873 AC: 127AN: 1454542Hom.: 0 Cov.: 29 AF XY: 0.0000953 AC XY: 69AN XY: 724262
GnomAD4 genome AF: 0.000210 AC: 32AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74412
ClinVar
Submissions by phenotype
Non-ketotic hyperglycinemia Benign:3
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 24, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at