ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.1176C>G (p.Gly392=) (rs1800727)

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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000130991 SCV000185914 benign Hereditary cancer-predisposing syndrome 2014-11-25 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics,PreventionGenetics RCV000247410 SCV000301650 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000386773 SCV000367026 benign Ataxia-telangiectasia syndrome 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV000386773 SCV000558356 benign Ataxia-telangiectasia syndrome 2020-11-23 criteria provided, single submitter clinical testing
Color Health, Inc RCV000130991 SCV000681955 benign Hereditary cancer-predisposing syndrome 2015-04-02 criteria provided, single submitter clinical testing
Counsyl RCV000386773 SCV000797300 benign Ataxia-telangiectasia syndrome 2018-01-19 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001289909 SCV001477910 benign none provided 2020-03-20 criteria provided, single submitter clinical testing
GeneDx RCV001705930 SCV001833949 benign not provided 2015-03-03 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 17333338)
True Health Diagnostics RCV000130991 SCV000787841 likely benign Hereditary cancer-predisposing syndrome 2018-02-23 no assertion criteria provided clinical testing
Natera, Inc. RCV000386773 SCV001456883 benign Ataxia-telangiectasia syndrome 2020-09-16 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001354336 SCV001548931 benign Bile duct cancer no assertion criteria provided clinical testing The ATM p.Gly392= variant was identified in dbSNP (ID: rs1800727) as “With other allele”, ClinVar (classified benign by Ambry Genetics, Prevention Genetics and Invitae, and likely benign by Illumina), Clinvitae (3x), Cosmic (2x in a haematopoietic neoplasm), LOVD 3.0, and in control databases in 1348 (34 homozygous) of 276972 chromosomes at a frequency of 0.005, increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include African in 1208 (34 homozygous) of 24022 chromosomes (freq: 0.05), Other in 22 of 6456 chromosomes (freq: 0.003), Latino in 90 of 34396 chromosomes (freq: 0.003), and European in 28 of 126546 chromosomes (freq: 0.0002), while it not observed in the Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. The variant was not identified in GeneInsight-COGR or the MutDB database. The p.Gly392= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000247410 SCV001808204 benign not specified no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute RCV000247410 SCV001905971 benign not specified no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000247410 SCV001918461 benign not specified no assertion criteria provided clinical testing

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