ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.5497-8T>C (rs3092829)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000119146 SCV000153865 benign Ataxia-telangiectasia syndrome 2020-11-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV000128919 SCV000172786 benign Hereditary cancer-predisposing syndrome 2013-05-29 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.
Vantari Genetics RCV000128919 SCV000266993 benign Hereditary cancer-predisposing syndrome 2015-10-23 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000246719 SCV000301673 benign not specified criteria provided, single submitter clinical testing
Color Health, Inc RCV000128919 SCV000537354 benign Hereditary cancer-predisposing syndrome 2015-04-02 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001282607 SCV000602563 benign none provided 2020-08-10 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000119146 SCV000743731 likely benign Ataxia-telangiectasia syndrome 2014-10-09 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000119146 SCV001260629 benign Ataxia-telangiectasia syndrome 2018-03-08 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam RCV000119146 SCV000745817 benign Ataxia-telangiectasia syndrome 2015-11-22 no assertion criteria provided clinical testing
True Health Diagnostics RCV000128919 SCV000787872 likely benign Hereditary cancer-predisposing syndrome 2018-01-12 no assertion criteria provided clinical testing
Natera, Inc. RCV000119146 SCV001452318 benign Ataxia-telangiectasia syndrome 2020-09-16 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001357689 SCV001553231 benign Malignant tumor of breast no assertion criteria provided clinical testing The ATM c.5497-8T>C variant was identified in 37 of 1416 proband chromosomes (frequency: 0.026) from individuals or families with breast cancer (Concannon 2008, Paglia 2010). The variant was also identified in dbSNP (ID: rs3092829) as “With Benign allele”, ClinVar (5x, as benign by Invitae, Ambry Genetics, Vantari, PreventionGenetics, Color Genomics), Clinvitae (3x, as benign), Cosmic (4x, in ovary carcinoma, and soft tissue Haemangioblastoma), LOVD 3.0 (1x with "does not affect function"), databases. The variant was not identified in GeneInsight-COGR, MutDB and ATM-LOVD, databases. The variant was identified in control databases in 6238 (94 homozygous) of 276468 chromosomes at a frequency of 0.0225 increasing the likelihood this could be a benign variant (Genome Aggregation Consortium Feb 27, 2017). The variant was identified in the following populations at a frequency greater than 1%: European (Non-Finnish) in 4209 (69 homozygous) of 126224 chromosomes (freq: 0.033), other in 181 (3 homozygous) of 6446 chromosomes (freq: 0.028), European (Finnish) in 650 (10 homozygous) of 25722 chromosomes (freq: 0.025), Ashkenazi Jewish* in 236 (4 homozygous) of 10138 chromosomes (freq: 0.023), Latino in 631 (7 homozygous) of 34354 chromosomes (freq: 0.018). The c.5497-8T>C variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions. However, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. However, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001358036 SCV001553673 benign Triple-negative breast carcinoma no assertion criteria provided clinical testing The ATM c.5497-8T>C variant was identified in 37 of 1416 proband chromosomes (frequency: 0.026) from individuals or families with breast cancer (Concannon 2008, Paglia 2010). The variant was also identified in dbSNP (ID: rs3092829) as “With Benign allele”, ClinVar (5x, as benign by Invitae, Ambry Genetics, Vantari, PreventionGenetics, Color Genomics), Clinvitae (3x, as benign), Cosmic (4x, in ovary carcinoma, and soft tissue Haemangioblastoma), LOVD 3.0 (1x with "does not affect function"), databases. The variant was not identified in GeneInsight-COGR, MutDB and ATM-LOVD, databases. The variant was identified in control databases in 6238 (94 homozygous) of 276468 chromosomes at a frequency of 0.0225 increasing the likelihood this could be a benign variant (Genome Aggregation Consortium Feb 27, 2017). The variant was identified in the following populations at a frequency greater than 1%: European (Non-Finnish) in 4209 (69 homozygous) of 126224 chromosomes (freq: 0.033), other in 181 (3 homozygous) of 6446 chromosomes (freq: 0.028), European (Finnish) in 650 (10 homozygous) of 25722 chromosomes (freq: 0.025), Ashkenazi Jewish* in 236 (4 homozygous) of 10138 chromosomes (freq: 0.023), Latino in 631 (7 homozygous) of 34354 chromosomes (freq: 0.018). The c.5497-8T>C variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions. However, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. However, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.

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