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 computed assertion could be determined for this classification!

Variant: NM_001482.3(GATM):c.156T>A (p.Ala52=)

CA7542986

469137 (ClinVar)

Gene: GATM
Condition: AGAT deficiency
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 3658ea5c-6197-436c-a523-9a4486982f04
Approved on: 2024-11-08
Published on: 2024-11-13

HGVS expressions

NM_001482.3:c.156T>A
NM_001482.3(GATM):c.156T>A (p.Ala52=)
NC_000015.10:g.45376733A>T
CM000677.2:g.45376733A>T
NC_000015.9:g.45668931A>T
CM000677.1:g.45668931A>T
NC_000015.8:g.43456223A>T
NG_011674.1:g.7050T>A
NG_011674.2:g.30585T>A
ENST00000396659.8:c.156T>A
ENST00000674905.1:c.156T>A
ENST00000675158.1:c.156T>A
ENST00000675323.1:c.156T>A
ENST00000675701.1:c.96T>A
ENST00000675974.1:n.247T>A
ENST00000676090.1:c.315T>A
ENST00000396659.7:c.156T>A
ENST00000558118.1:c.156T>A
ENST00000558163.1:c.69+1652T>A
ENST00000558336.5:c.156T>A
ENST00000558362.5:n.1812T>A
ENST00000558537.5:c.-232T>A
ENST00000559885.1:c.-232T>A
ENST00000560538.1:n.425T>A
ENST00000561148.5:c.-232T>A
NM_001482.2:c.156T>A
NM_001321015.1:c.-232T>A
NM_001321015.2:c.-232T>A
More

Likely Benign

Met criteria codes 2
BP4 BS1
Not Met criteria codes 1
BP7

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 GATM Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_001482.3:c.156T>A variant in GATM is a synonymous (silent) variant (p.Ala52=). The computational predictor, SpliceAI, predicts that the variant does not impact splicing (BP4). BP7 was not applied because the nucleotide is moderately conserved, as shown by phyloP (score 2.27). To our knowledge, this variant has not been reported in the literature and results of functional studies are unavailable. The highest population minor allele frequency in gnomAD v2.1.1 is 0.00016 (4/24964 alleles) in the African population, which is higher than the ClinGen CCDS VCEP’s threshold for BS1 (>0.0001), and therefore meets this criterion (BS1). There is a ClinVar entry for this variant (Variation ID: 469137). In summary, this variant meets the criteria to be classified as likely benign for AGAT deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): BS1, BP4. Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on November 8, 2024)
Met criteria codes
BP4
The computational predictor, SpliceAI, predicts that the variant does not impact splicing (BP4).
BS1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00016 (4/24964 alleles) in the African population, which is higher than the ClinGen CCDS VCEP’s threshold for BS1 (>0.0001), and therefore meets this criterion (BS1).
Not Met criteria codes
BP7
The NM_001482.3:c.156T>A variant in GATM is a synonymous (silent) variant (p.Ala52=). BP7 was not applied because the nucleotide is moderately conserved, as shown by phyloP (score 2.27).
Curation History
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