Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!

Variant: NM_000156.6(GAMT):c.570+4C>T

CA9043611

582572 (ClinVar)

Gene: GAMT
Condition: guanidinoacetate methyltransferase deficiency
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 9d10fd24-b5da-4e45-8e8a-53133df173e9
Approved on: 2024-09-11
Published on: 2024-09-12

HGVS expressions

NM_000156.6:c.570+4C>T
NM_000156.6(GAMT):c.570+4C>T
NC_000019.10:g.1398912G>A
CM000681.2:g.1398912G>A
NC_000019.9:g.1398911G>A
CM000681.1:g.1398911G>A
NC_000019.8:g.1349911G>A
NG_009785.1:g.7642C>T
ENST00000252288.8:c.570+4C>T
ENST00000447102.8:c.574C>T
ENST00000591788.3:c.253+4C>T
ENST00000640164.1:n.403+4C>T
ENST00000640762.1:c.501+4C>T
ENST00000252288.6:c.570+4C>T
ENST00000447102.7:c.574C>T
ENST00000591788.2:c.255+4C>T
NM_000156.5:c.570+4C>T
NM_138924.2:c.574C>T
NM_138924.3:c.574C>T
More

Likely Benign

Met criteria codes 2
BS1 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Cerebral Creatine Deficiency Syndromes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GAMT Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_000156.6:c.570+4C>T variant in GAMT is an intronic variant affecting a nucleotide within the consensus splice site of intron 5. To our knowledge, this variant has not been reported in the literature and results of functional studies are unavailable. The highest population frequency in gnomAD v4.1.0. is 0.001148 (86/74912 alleles; no homozygotes) in the African / Afircan American population, which is higher than the ClinGen CCDS VCEP’s threshold for BS1 (>0.001), and therefore meets this criterion (BS1). The computational splicing predictor SpliceAI gives a score of 0.01 for donor loss and suggests that the variant has no impact on splicing (BP4). There is a ClinVar entry for this variant (Variation ID: 582572). In summary, this variant meets the criteria to be classified as likely benign for GAMT deficiency. GAMT-specific ACMG/AMP codes met, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes VCEP (Specifications Version 2.0.0): BS1, BP4. (Classification approved by the ClinGen Creatine Deficiency Syndromes Variant Curation Expert Panel on September 11, 2024).
Met criteria codes
BS1
The highest population frequency in gnomAD v2.1.1 is 0.00101 (25/24798 alleles) in the African population, which is higher than the ClinGen CCDS VCEP’s threshold for BS1 (>0.001), and therefore meets this criterion (BS1).
BP4
The computational splicing predictor SpliceAI gives a score of 0.01 for donor loss and suggests that the variant has no impact on splicing (BP4).
Curation History
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