rs371511930
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000156.6(GAMT):c.328-10C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000151 in 1,611,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000156.6 splice_polypyrimidine_tract, intron
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 | UniProt |
---|---|---|---|---|---|---|---|
GAMT | NM_000156.6 | c.328-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000252288.8 | |||
GAMT | NM_138924.3 | c.328-10C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAMT | ENST00000252288.8 | c.328-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000156.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000126 AC: 31AN: 245432Hom.: 0 AF XY: 0.0000901 AC XY: 12AN XY: 133194
GnomAD4 exome AF: 0.000148 AC: 216AN: 1459154Hom.: 0 Cov.: 32 AF XY: 0.000158 AC XY: 115AN XY: 725740
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74480
ClinVar
Submissions by phenotype
Deficiency of guanidinoacetate methyltransferase Uncertain:1
Uncertain significance, 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 24, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 18, 2021 | This variant is associated with the following publications: (PMID: 26003046) - |
Cerebral creatine deficiency syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at