ClinVar Miner

Submissions for variant NC_012920.1(MT-ATP6):m.9055G>A

dbSNP: rs193303045
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel, ClinGen RCV001796802 SCV002037587 benign Mitochondrial disease 2021-10-26 reviewed by expert panel curation The m.9055G>A (p.A177T) variant in MT-ATP6 is a missense variant that reaches benign stand-alone criteria (BA1). The highest population minor allele frequency in GenBank (51,863 GenBank sequences) is 4.24%; in gnomad v3.1.2 is 5.393% (homoplasmic occurrences); and in Helix (196,554 sequences, 91% lineage N bias) is 8.05%. These are all higher than the ClinGen Mitochondrial Disease Nuclear and Mitochondrial Variant Curation Expert Panel - mtDNA specifications - threshold (>0.01 or 1%). Furthermore, m.9055G>A is a haplogroup-defining variant for K at 99.7%. It is also found in Z3b (100%) and U8b (100%). Therefore, this meets this criterion (BA1). As a note, the K haplogroup is common in the Ashkenazi Jewish population. m.9055 G>A is a haplogroup-defining variant for K at 99.7%. Subgroup frequencies are K1 (99.3%) and K2 (99.7%). Additionally, the computational predictor APOGEE gives a consensus rating of neutral with an extremely low pathogenicity predictor score, 0.2 (Min=0, Max=1), evidence that does not predict a damaging effect on gene function (BP4). In summary, this variant meets criteria to be classified as benign for primary mitochondrial disease inherited in a mitochondrial manner. However, if this variant is identified in an individual who is a member of a different haplogroup than described above, consider further evaluation of this variant. This classification was approved by the NICHD U24 Mitochondrial Disease Variant Curation Expert Panel on May 20, 2021. Mitochondrial DNA-specific ACMG/AMP criteria applied: BA1, BP4.
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine RCV000854413 SCV000997448 benign Leigh syndrome 2019-10-17 criteria provided, single submitter clinical testing The NC_012920.1:m.9055G>A (YP_003024031.1:p.Ala177Thr) variant in MTATP6 gene is interpretated to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BA1

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