3-37012071-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BS3BS1BP5
This summary comes from the ClinGen Evidence Repository: The NM_000249.4(MLH1):c.649C>T (p.Arg217Cys) variant is a missense variant predicted to cause substitution of Arginine by Cystein at amino acid 217 (p.Arg217Cys). The allele frequency of the variant c.649C>T is 0.3% (PopMax Filtering AF 0.0037 in East Asian Population) for the total non-cancer dataset from gnomAD (v2.1.1), and gnomAD v4.1 Grpmax AF is 0.003970 which is higher than the ClinGen InSiGHT MMR VCEP threshold (≥ 0.001 or 0,1%) for BS1, and therefore meets this criterion (BS1).The CIMRA Functional Odds for Pathogenicity is 0.01 which is below the VCEP threshold of ≤ 0.052 (BS3 met).Also the variant has been detected in 2 or 3 tumours: CRC/Endometrial tumours with MSS and/or no loss of MMR protein expression and/or LS spectrum tumoursf with loss of MMR protein(s) that is inconsistent with the gene demonstrating genetic variation (BP5 met).In summary, this variant meets the criteria to be classified as benign for autosomal-dominant inherited Lynch syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP : criteria BS2, BS3 and BP5 applied. (VCEP specifications version 1) LINK:https://erepo.genome.network/evrepo/ui/classification/CA011361/MONDO:0007356/115
Frequency
Consequence
NM_001167618.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.0000986 AC: 15AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000370 AC: 93AN: 251150Hom.: 0 AF XY: 0.000309 AC XY: 42AN XY: 135720
GnomAD4 exome AF: 0.000137 AC: 200AN: 1461518Hom.: 0 Cov.: 30 AF XY: 0.000150 AC XY: 109AN XY: 727090
GnomAD4 genome 0.0000985 AC: 15AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:4
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This variant is associated with the following publications: (PMID: 8581513, 11555625, 17594722, 21901500, 11920458, 27487738, 29752822, 32601921, 23760103, 11781295, 20176959, 17510385, 22949387, 12810663, 27553368, 18094436, 8797773, 9559627, 15613555, 16425354, 22136435, 17074586, 27173243, 28452373, 28389907, 29505604, 28767289, 31010795, 30740464, 30521064, 30850667, 31386297, 31784484) -
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Hereditary cancer-predisposing syndrome Benign:3
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. -
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Colorectal cancer, hereditary nonpolyposis, type 2 Uncertain:1Benign:1
This variant is considered 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]. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance. -
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. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
not specified Benign:2
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Variant summary: MLH1 c.649C>T (p.Arg217Cys) results in a non-conservative amino acid change located in the N-terminal domain (IPR002099) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. 4/4 computational tools predict no significant impact on normal splicing. The variant allele was found at a frequency of 0.00041 in 252977 control chromosomes, predominantly at a frequency of 0.0047 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 7 fold of the estimated maximal expected allele frequency for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer phenotype (0.00071), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.649C>T has also been reported in the literature in several individuals affected with Lynch Syndrome, who were predominantly of Asian descent and the majority of these publications only performed evaluation of MLH1 and could not rule out variants in other Lynch syndrome associated genes. These reports therefore do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. In addition, in one publication (Sapari 2014), the variant was found in co-occurrence with another pathogenic MLH1 variant, c.790+1G>A (although it was only identified through NGS and not confirmed by Sanger sequencing). One co-occurrence with another pathogenic variant has been reported internally (BRCA2 c.1648G>T , p.Glu550X), providing supporting evidence for a benign role. Several publications reported experimental evidence evaluating an impact on protein function (Ellison 2001, Trojan 2002, Kondo 2003, Takahashi 2007, Zhao 2008, Peng 2016), showing no or only a mild effect on function. A recent study suggested based on in vitro evidence that the variant might affect splicing by affecting splicesome assembly (Rhine 2018), however earlier reports that identified the variant in patients through RNA-based direct sequencing, did not indicate any specific splicing effect (Furukawa 2002, Wang 2005); therefore, the significance of this finding is uncertain. The following publications have been ascertained in the context of this evaluation (PMID: 12810663, 18373977, 11555625, 8797773, 18069769, 17510385, 9419403, 15342696, 8581513, 11781295, 15613555, 11920458, 24933000, 25882375, 21901500, 27553368, 22136435, 16425354, 27173243, 27093186, 25338684, 28767289, 29050249, 29505604, 30850667, 31666926). Nine submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified as benign/likely benign (n=7) and VUS (n=2). Based on the evidence outlined above, the variant was classified as benign. -
Lynch syndrome 1 Uncertain:1
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Hereditary breast ovarian cancer syndrome Uncertain:1
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Carcinoma of colon Benign:1
The MLH1 p.Arg217Cys variant was identified in 12 of 656 proband chromosomes (frequency: 0.02) from individuals or families with Extramammary Paget disease or sporadic colorectal cancer and was present in 8 of 1260 control chromosomes (frequency: 0.006) from healthy individuals (Kang 2016, Peng 2015). The variant was also identified in dbSNP (ID: rs4986984) as "With other allele”, ClinVar (classified as benign by Color; as likely benign by Invitae, GeneDx, Ambry Genetics and one clinical laboratory; as uncertain significance by two clinical laboratories), Cosmic (4x in Skin or bone tissue), MutDB , UMD-LSDB (2x as neutral), Zhejiang University Database, Mismatch Repair Genes Variant Database, and in Insight Hereditary Tumors (42x as uncertain) databases. The variant was not identified in COGR database. The variant was identified in control databases in 91 of 276864 chromosomes at a frequency of 0.0003 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: European in 2 of 126374 chromosomes (freq: 0.00002), East Asian in 83 of 18868 chromosomes (freq: 0.004), and South Asian in 6 of 30782 chromosomes (freq: 0.0002), while the variant was not observed in the African, Other, Latino, Ashkenazi Jewish, and Finnish, populations. The p.Arg217 residue is conserved in mammals but not in more distantly related organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume 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. Several functional studies identified the variant might affect the MMR process at different levels and might have functional relation to gastrointestinal cancer. The variant showed variable levels of MMR activity (50%, 64.8%, or 81.3%) compare to WT however overall the studies concluded that although efficiency of MMR is slightly reduced it is still proficient (Kang 2016, Lucci-Cordisco 2006, Fan 2007, Takahashi 2007, Trojan 2002). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. -
MLH1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Hereditary nonpolyposis colorectal neoplasms Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at