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.1041C>T (p.Asp347=)

CA291039

137450 (ClinVar)

Gene: GATM
Condition: AGAT deficiency
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 334563f7-be38-4e07-98a2-59a1f900f20d
Approved on: 2024-08-20
Published on: 2024-09-20

HGVS expressions

NM_001482.3:c.1041C>T
NM_001482.3(GATM):c.1041C>T (p.Asp347=)
NC_000015.10:g.45364798G>A
CM000677.2:g.45364798G>A
NC_000015.9:g.45656996G>A
CM000677.1:g.45656996G>A
NC_000015.8:g.43444288G>A
NG_011674.1:g.18985C>T
NG_011674.2:g.42520C>T
ENST00000396659.8:c.1041C>T
ENST00000674905.1:c.1041C>T
ENST00000675158.1:c.1041C>T
ENST00000675323.1:c.1041C>T
ENST00000675701.1:c.981C>T
ENST00000675974.1:n.1132C>T
ENST00000676090.1:c.*1772C>T
ENST00000396659.7:c.1041C>T
ENST00000558336.5:c.1041C>T
ENST00000558362.5:n.2697C>T
ENST00000561376.1:n.88C>T
NM_001482.2:c.1041C>T
NM_001321015.1:c.654C>T
NM_001321015.2:c.654C>T
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Benign

Met criteria codes 1
BA1
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.1041C>T variant in GATM is a synonymous (silent) variant (p.Asp347=). SpliceAI does not predict an impact on splicing, but BP7 was not applied because the nucleotide is conserved (GERP score > 5). 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 0.00101 (31/30616 alleles) in the South Asian population, which is higher than the ClinGen CCDS VCEP’s threshold for BA1 (>0.0005), and therefore meets this criterion (BA1). There is a ClinVar entry for this variant (Variation ID: 137450). In summary, this variant meets the criteria to be classified as 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): BA1. (Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on August 20, 2024).
Met criteria codes
BA1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00101 (31/30616 alleles) in the South Asian population, which is higher than the ClinGen CCDS VCEP’s threshold for BA1 (>0.0005), and therefore meets this criterion (BA1).
Not Met criteria codes
BP7
The NM_001482.3:c.1041C>T variant in GATM is a synonymous (silent) variant (p.Asp347=). SpliceAI does not predict an impact on splicing, but BP7 was not applied because the nucleotide is conserved (GERP score > 5).
Curation History
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