Submissions for variant NM_000249.4(MLH1):c.1897-2A>G

dbSNP: rs267607871

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075411	SCV000106407	likely pathogenic	Lynch syndrome	2019-06-21	reviewed by expert panel	curation	Interrupts canonical donor splice site
GeneDx	RCV000487325	SCV000565163	uncertain significance	not provided	2023-06-20	criteria provided, single submitter	clinical testing	Canonical splice variant demonstrated to result in a minor splice defect that may not impact protein function (External communication with outside laboratory); Not observed at significant frequency in large population cohorts (gnomAD); Observed in individuals with colon cancer (Rajkumar et al., 2004; Pearlman et al., 2017; Yurgelun et al., 2017); This variant is associated with the following publications: (PMID: 28135145, 27978560, 15345113, 22753075, 20533529, 12799449, 30720243, 30787465, 33087929, 35710434)
Invitae	RCV000524638	SCV000625106	uncertain significance	Hereditary nonpolyposis colorectal neoplasms	2023-12-20	criteria provided, single submitter	clinical testing	This sequence change affects an acceptor splice site in intron 16 of the MLH1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in the gain of 1 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is present in population databases (rs267607871, gnomAD 0.0009%). Disruption of this splice site has been observed in individual(s) with colorectal cancer (PMID: 15345113, 27978560, 28135145). This variant is also known as IVS16-2A>G. ClinVar contains an entry for this variant (Variation ID: 89932). Studies have shown that disruption of this splice site results in the activation of a cryptic splice site in intron 16 (Invitae). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics	RCV000570210	SCV000669547	uncertain significance	Hereditary cancer-predisposing syndrome	2023-04-18	criteria provided, single submitter	clinical testing	The c.1897-2A>G intronic variant results from an A to G substitution two nucleotides upstream from coding exon 17 in the MLH1 gene. This alteration has been identified in two probands with early-onset colorectal cancer, one of whom had a MSI-high tumor and met Bethesda criteria for Lynch syndrome; however, the colon tumor of the second proband was reported to be mismatch repair (MMR) proficient demonstrating microsatellite stability and/or normal immunohistochemistry (Rajkumar T et al. Genet. Test. 2004 ;8(2):157-62; Pearlman R et al. JAMA Oncol. 2017 Apr;3(4):464-471). This variant was also reported in an individual from a cohort of unselected colorectal cancer patients undergoing multigene panel testing (Yurgelun MB et al. J. Clin. Oncol. 2017 Apr;35:1086-1095). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and may result in the creation or strengthening of a novel splice acceptor site. RNA studies have demonstrated that this alteration results in a transcript predicted to lead to a protein with an in-frame insertion of one amino acid that is structurally deleterious (Ambry internal data). Of note, this alteration is also designated as IVS16-2A>G in the published literature. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001844029	SCV000696134	uncertain significance	not specified	2022-02-27	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.1897-2A>G alters a conserved nucleotide located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes the canonical 3' splice acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4e-06 in 251356 control chromosomes. c.1897-2A>G has been reported in the literature as a VUS in individuals affected with colorectal cancer (Pearlman 2017, Yurgelun 2017), although in one of these cases the associated tumor was described as MMR proficient (based on microsatellite instability and/or immunohistochemistry) (Pearlman 2017). The variant appeared to segregate with the disease in a family that fulfilled the Bethesda guidelines for Lynch Syndrome (Rajkumar 2004), and though the tumor status here was described as MMR deficient (assessed by high microsatellite instability), in these patients only MLH1 and MSH2 was studied. These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six clinical diagnostic laboratories and an expert panel (International Society for Gastrointestinal Hereditary Tumours, InSiGHT) have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (Likely Pathogenic, n=6 including the expert panel, VUS, n=1). One submitter reports a VUS classification having re-classified it from Likely Pathogenic as an outcome of RNA analysis demonstrating no impact on splicing at their laboratory. Based on the evidence outlined above, the variant was re-classified as VUS possibly pathogenic.
Counsyl	RCV000662785	SCV000785594	likely pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2017-09-29	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV000763104	SCV000893646	likely pathogenic	Mismatch repair cancer syndrome 1; Muir-Torré syndrome; Colorectal cancer, hereditary nonpolyposis, type 2	2018-10-31	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000570210	SCV000908649	uncertain significance	Hereditary cancer-predisposing syndrome	2023-05-12	criteria provided, single submitter	clinical testing	This variant causes an A to G nucleotide substitution at the -2 position of intron 16 of the MLH1 gene. Splice site prediction tools suggest that this variant would impact splicing at the intron 16 splice acceptor site. An external laboratory has reported that this variant activates a cryptic, in-frame splice acceptor site, 3 bp upstream from the canonical acceptor site, that results in a majority transcript predicted to produce a protein with an in-frame insertion of one amino acid (p.Glu632_Glu633insArg) (ClinVar SCV000669547.5). To our knowledge functional studies have not been reported for MLH1 p.Glu632_Glu633insArg, and the functional consequence of this change is unknown, although the change does occur in a conserved region of the EXO1/PMS2/MLH3/PMS1-interacting domain. This variant has been reported in two related individuals affected with Lynch syndrome (PMID: 15345113), and two unrelated individuals affected with colorectal cancer, one of whom was affected with early-onset colorectal cancer (age <50) with a mismatch repair proficient tumor (PMID: 27978560, 28135145). However, the variant has also been seen in unaffected individuals and individuals with non-Lynch Syndrome cancers (DOI: 10.1016/j.gim.2022.01.077, external laboratory communication, Color internal data). This variant has been identified in 1/251356 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may have a pathogenic role, additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Revvity Omics, Revvity	RCV000487325	SCV003808830	uncertain significance	not provided	2023-03-01	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV000662785	SCV004018625	likely benign	Colorectal cancer, hereditary nonpolyposis, type 2	2023-11-14	criteria provided, single submitter	clinical testing	This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 27363726].
Baylor Genetics	RCV000662785	SCV004195047	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2023-10-18	criteria provided, single submitter	clinical testing