The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • The variant label for this record ("m.7471delC") does not appear to be in HGVS format
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MT-TS1 CSPEC Genes: [] * Message MONDOs: MONDO:0044970 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!


Variant: m.7471delC

CA131012

42227 (ClinVar)

Gene: MT-TS1
Condition: mitochondrial disease
Inheritance Mode: Mitochondrial inheritance
UUID: 540a3490-b704-4bee-995c-4c24d120851d
Approved on: 2023-05-22
Published on: 2024-03-28

HGVS expressions

NC_012920.1:m.7471del
J01415.2:m.7471del

Uncertain Significance

Not Met criteria codes 7
PM6 PM2 BP4 PS2 PS3 PS4 PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Mitochondrial Disease Nuclear and Mitochondrial Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1_mtDNA

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The m.7471delC variant in MT-TS1 was reviewed by the Mitochondrial Disease Variant Curation Expert Panel on May 22, 2023. This variant has not been reported in the medical literature as causative in affected individuals or families with primary mitochondrial disease to our knowledge. This variant is present in population databases (Mitomap's 28/59,389 sequences: AF= 0.047%; Helix's 162/195,983 sequences: AF=0.070% including 137 homoplasmic occurrences in addition to 25 heteroplasmic occurrences, and in haplogroups H, U, T, K, B, D, M, HV, J, A, I, X, T, C, K, M, W, V; and gnomAD v3.1.2: AF=0.053 % including 30 homoplasmic occurrences in addition to five heteroplasmic occurrences). Given the frequency of this variant, it does not meet PM2 criterion. The computational predictor MitoTIP suggests this variant is benign (4.3 percentile) and HmtVAR does not provide a prediction. Given the lack of computational evidence, BP4 cannot be applied. There are no cybrids, single fiber studies, or other functional assays reported on this variant. In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner. We note that three experts on this panel felt likely benign was a more appropriate classification given the presence in the general population however the majority (four) agreed with uncertain significance. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on May 22, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): None.
Not Met criteria codes
PM6
There are no reported de novo occurrences of this variant to our knowledge.
PM2
This variant is present in population databases (Mitomap's 28/59,389 sequences: AF= 0.047%; Helix's 162/195,983 sequences: AF=0.070% 137 homoplasmic and 25 heteroplasmic; haplogroups H, U, T, K, B, D, M, HV, J, A, I, X, T, C, K, M, W, V; and gnomAD v3.1.2: AF=0.053 % as this is homoplasmic in 30 individuals and heteroplasmic in 5 individuals). Given the frequency of this variant, it does not meet PM2 criterion.
BP4
The computational predictor MitoTIP suggests this variant is benign (4.3 percentile) and HmtVAR does not provide a prediction. Given the lack of computational evidence BP4 criteria can not be applied.
PS2
There are no reported de novo occurrences of this variant to our knowledge.
PS3
There are no cybrids, single fiber studies, or other functional assays reported on this variant.
PS4
There are no individuals with this variant reported in the medical literature to our knowledge.
PP1
There are no large families reported in the medical literature to consider for evidence of segregation.
Curation History
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