Submissions for variant NM_000249.4(MLH1):c.546-1G>A

dbSNP: rs587779022

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075754	SCV000106766	likely pathogenic	Lynch syndrome	2019-06-21	reviewed by expert panel	curation	Interrupts canonical donor splice site
GeneDx	RCV000482173	SCV000568562	pathogenic	not provided	2017-01-02	criteria provided, single submitter	clinical testing	This variant is denoted MLH1 c.546-1G>A or IVS6-1G>A and consists of a G>A nucleotide substitution at the -1 position of intron 6 of the MLH1 gene. This variant destroys a canonical splice acceptor site and is predicted to cause abnormal gene splicing, leading to either an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product. This variant has been reported in at least one Lynch syndrome family (Domingo 2004). Based on the current evidence, we consider this variant to be pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001854304	SCV002294839	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2023-12-18	criteria provided, single submitter	clinical testing	This sequence change affects an acceptor splice site in intron 6 of the MLH1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in MLH1 are known to be pathogenic (PMID: 15713769, 24362816). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with clinical features of Lynch syndrome (PMID: 10732761, 15342696; Invitae). ClinVar contains an entry for this variant (Variation ID: 90265). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV002271399	SCV002556258	likely pathogenic	Hereditary nonpolyposis colon cancer	2022-06-30	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.546-1G>A is 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 was absent in 251222 control chromosomes. c.546-1G>A has been reported in the literature as a germline variant in at-least one individual with MSI-high Lynch Syndrome and supportive IHC findings (example, Cunningham_1998 cited in Domingo_2004) and among pathogenic/likely pathogenic variants of somatic origin in at-least one individual with endometrioid adenocarcinoma and absent MLH1/PMS2 on IHC who was identified as a suitable referral to the familial cancer clinic based solely on reflex Lynch syndrome screening (example, Najdawi_2017). At least one publication reports experimental evidence evaluating an impact on mismatch repair activity following exposure of mouse embryonic stem cells to 6-thioguanine, however, does not allow convincing conclusions about the variant effect due to intermediate results (Houlleberghs_2020). Two 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. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Ambry Genetics	RCV003162487	SCV003884686	likely pathogenic	Hereditary cancer-predisposing syndrome	2024-02-05	criteria provided, single submitter	clinical testing	The c.546-1G>A intronic variant results from a G to A substitution one nucleotide upstream from coding exon 7 of the MLH1 gene. This alteration was identified in an individual from a Lynch syndrome family whose colon tumor was negative for the BRAF V600E mutation (Domingo E et al. J Med Genet, 2004 Sep;41:664-8). In addition, this alteration has been observed in at least one individual with a personal and/or family history that is consistent with Lynch syndrome (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.
Myriad Genetics, Inc.	RCV003452746	SCV004186440	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-14	criteria provided, single submitter	clinical testing	This variant is considered pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 12052501].