ClinVar Genomic variation as it relates to human health

DNA sequence analysis of the ATM gene demonstrated a sequence change, c.7502A>G, in exon 50 that results in an amino acid change, p.Asn2501Ser. This sequence change does not appear to have been previously described in patients with ATM-related disorders and has been described in the gnomAD database with a frequency of 0.12% in the South Asian population (dbSNP rs531617441). The p.Asn2501Ser change affects a highly conserved amino acid residue located in a domain of the ATM protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Asn2501Ser substitution. Due to these contrasting evidences and the lack of functional studies, the clinical significance of the p.Asn2501Ser change remains unknown at this time.

Variant summary: ATM c.7502A>G (p.Asn2501Ser) results in a conservative amino acid change located in the PIK-related kinase domain (IPR014009) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00017 in 251096 control chromosomes, predominantly at a frequency of 0.0012 within the South Asian subpopulation in the gnomAD database. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 1.2 fold of the estimated maximal expected allele frequency for a pathogenic variant in ATM causing Breast Cancer phenotype (0.001), strongly suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. c.7502A>G has been reported in the literature as a VUS in settings of multigene panel testing in unaffected Japanese male control individuals but not in cases affected with Breast Cancer (example, Momozawa_2018) and also in cases with breast cancer and unaffected controls in another study (example, Dorling_2021). These report(s) do not provide unequivocal conclusions about association of the variant with Breast Cancer. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (VUS, n=10; Likely benign, n=1). Based on the evidence outlined above, the variant was classified as likely benign.

The observed missense chr11:g.108201135A>G variant in ATM gene has been reported previously in heterozygous state in individual(s) affected with Indian Hereditary Breast and Ovarian Cancer (Kadri et al., 2021). This variant is reported with the allele frequency of 0.02% in the gnomAD Exomes. This variant has been reported to the ClinVar database with varying interpretation: Likely Benign / Uncertain Significance (multiple submitters). However, no details are available for independent assessment. The amino acid Asn at position 2501 is changed to a Ser changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Asn2501Ser in ATM is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. Computational evidence (Polyphen - Damaging, SIFT - Tolerated, and MutationTaster - Disease causing) predicts conflicting evidence on protein structure and function for this variant. For these reasons, this variant has been classified as Uncertain Significance.

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.

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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25326635, 30287823, 28652578, 33552952, 37277882, 23532176, 36243179, 29684080)

Likely pathogenicity based on finding it in trans with a known deleterious mutation in a 10-year-old male with global delays, myopathy, epilepsy, generalize muscle weakness, and abnormal brain MRI. Heterozygotes are expected to be asymptomatic carriers.

The ATM p.Asn2501Ser variant was identified in the literature in 12490 male controls with frequency 0.0001 and was not identified in 11241 female controls and 53 male and 7051 female breast cancer cases (Momozawa 2018). The variant was also identified in dbSNP (ID: rs531617441) as "With Uncertain significance allele", ClinVar (classified as uncertain significance by Invitae, Ambry Genetics and five other submitters), and in LOVD 3.0 (1x). The variant was identified in control databases in 46 of 276956 chromosomes at a frequency of 0.0002 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 24024 chromosomes (freq: 0.00004), Other in 1 of 6460 chromosomes (freq: 0.0002), Latino in 3 of 34414 chromosomes (freq: 0.00009), European in 2 of 126472 chromosomes (freq: 0.00002), and South Asian in 39 of 30782 chromosomes (freq: 0.001), while the variant was not observed in the Ashkenazi Jewish, East Asian, and Finnish, populations. The p.Asn2501 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.