Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_001482.3(GATM):c.*600A>G

CA10647042

316206 (ClinVar)

Gene: GATM

Condition: AGAT deficiency

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 536fa3c2-94e5-4a2b-9603-37252da50ac6

Approved on: 2022-06-06

Published on: 2022-10-05

HGVS expressions

NM_001482.3:c.*600A>G

NM_001482.3(GATM):c.*600A>G

NC_000015.10:g.45361509T>C

CM000677.2:g.45361509T>C

NC_000015.9:g.45653707T>C

CM000677.1:g.45653707T>C

NC_000015.8:g.43440999T>C

NG_011674.1:g.22274A>G

NG_011674.2:g.45809A>G

ENST00000396659.8:c.*600A>G

ENST00000675158.1:c.*772A>G

ENST00000675323.1:c.*2374A>G

ENST00000676090.1:c.*2603A>G

ENST00000396659.7:c.*600A>G

ENST00000558362.5:n.3528A>G

NM_001482.2:c.*600A>G

NM_001321015.1:c.*600A>G

NM_001321015.2:c.*600A>G

Benign

BA1

Evidence Links 0

Expert Panel

Cerebral Creatine Deficiency Syndromes VCEP

Criteria Specification Information

Criteria Specification: ClinGen Cerebral Creatine Deficiency Syndromes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GATM Version 1

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Cerebral Creatine Deficiency Syndromes VCEP

The NM_001482.3:c.*600A>G variant is a single nucleotide substitution in the 3'UTR of GATM. Because the variant is located in the 3'UTR, it is not expected to alter the amino acid sequence. The highest population minor allele frequency in gnomAD v2.1.1, in a continental population with >2000 alleles, is 0.2934 (2554/8704 alleles) in the African 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: 316206). 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 CCDS VCEP on June 6, 2022).

BA1

The highest population minor allele frequency in gnomAD v2.1.1, in a continental population with >2000 alleles, is 0.2934 (2554/8704 alleles) in the African population, which is higher than the ClinGen CCDS VCEP’s threshold for BA1 (>0.0005), and therefore meets this criterion (BA1).

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