ClinVar Miner

Submissions for variant NM_000156.6(GAMT):c.570+4C>T

gnomAD frequency: 0.00039  dbSNP: rs199967562
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000706678 SCV000835745 uncertain significance Cerebral creatine deficiency syndrome 2022-08-10 criteria provided, single submitter clinical testing This sequence change falls in intron 5 of the GAMT gene. It does not directly change the encoded amino acid sequence of the GAMT protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs199967562, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with GAMT-related conditions. ClinVar contains an entry for this variant (Variation ID: 582572). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV001613434 SCV001838282 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
New York Genome Center RCV001272269 SCV002548791 uncertain significance Deficiency of guanidinoacetate methyltransferase 2021-09-10 criteria provided, single submitter clinical testing
Ambry Genetics RCV002343573 SCV002650575 uncertain significance Inborn genetic diseases 2017-12-16 criteria provided, single submitter clinical testing The c.570+4C>T intronic variant results from a C to T substitution 4 nucleotides after coding exon 5 in the GAMT gene. This nucleotide position is not well conserved in available vertebrate species. Using two different splice site prediction tools, this alteration is predicted by BDGP to weaken the efficiency of the native splice donor site, but is not predicted to have a deleterious effect on this splice donor site by ESEfinder; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001272269 SCV001454098 uncertain significance Deficiency of guanidinoacetate methyltransferase 2020-09-16 no assertion criteria provided clinical testing

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