19-1397377-G-C
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000156.6(GAMT):āc.693C>Gā(p.Pro231Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,459,868 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 Likely benign (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0000034 ( 0 hom. )
Consequence
GAMT
NM_000156.6 synonymous
NM_000156.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.879
Genes affected
GAMT (HGNC:4136): (guanidinoacetate N-methyltransferase) The protein encoded by this gene is a methyltransferase that converts guanidoacetate to creatine, using S-adenosylmethionine as the methyl donor. Defects in this gene have been implicated in neurologic syndromes and muscular hypotonia, probably due to creatine deficiency and accumulation of guanidinoacetate in the brain of affected individuals. Two transcript variants encoding different isoforms have been described for this gene. Pseudogenes of this gene are found on chromosomes 2 and 13. [provided by RefSeq, Feb 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 19-1397377-G-C is Benign according to our data. Variant chr19-1397377-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3631446.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.879 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GAMT | ENST00000252288.8 | c.693C>G | p.Pro231Pro | synonymous_variant | Exon 6 of 6 | 1 | NM_000156.6 | ENSP00000252288.1 | ||
GAMT | ENST00000640762.1 | c.624C>G | p.Pro208Pro | synonymous_variant | Exon 6 of 6 | 5 | ENSP00000492031.1 | |||
GAMT | ENST00000640164.1 | n.*6C>G | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246930Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134226
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1459868Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 726268
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GnomAD4 genome Cov.: 33
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33
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cerebral creatine deficiency syndrome Benign:1
Nov 26, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at