3-37048515-A-G

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_ModeratePP5_Very_Strong

The NM_000249.4(MLH1):​c.1897-2A>G variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000891 in 1,459,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★★).

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000089 ( 0 hom. )

Consequence

MLH1
NM_000249.4 splice_acceptor, intron

Scores

5
1
1
Splicing: ADA: 1.000
1

Clinical Significance

Likely pathogenic reviewed by expert panel P:3U:8B:1

Conservation

PhyloP100: 8.70
Variant links:
Genes affected
MLH1 (HGNC:7127): (mutL homolog 1) The protein encoded by this gene can heterodimerize with mismatch repair endonuclease PMS2 to form MutL alpha, part of the DNA mismatch repair system. When MutL alpha is bound by MutS beta and some accessory proteins, the PMS2 subunit of MutL alpha introduces a single-strand break near DNA mismatches, providing an entry point for exonuclease degradation. The encoded protein is also involved in DNA damage signaling and can heterodimerize with DNA mismatch repair protein MLH3 to form MutL gamma, which is involved in meiosis. This gene was identified as a locus frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). [provided by RefSeq, Aug 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 10 ACMG points.

PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.04095112 fraction of the gene. Cryptic splice site detected, with MaxEntScore 5.5, offset of -3, new splice context is: cttgtcctttttcctgcaAGcgg. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PP5
Variant 3-37048515-A-G is Pathogenic according to our data. Variant chr3-37048515-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 89932.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37048515-A-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MLH1NM_000249.4 linkc.1897-2A>G splice_acceptor_variant, intron_variant Intron 16 of 18 ENST00000231790.8 NP_000240.1 P40692-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MLH1ENST00000231790.8 linkc.1897-2A>G splice_acceptor_variant, intron_variant Intron 16 of 18 1 NM_000249.4 ENSP00000231790.3 P40692-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251356
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135838
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000880
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000891
AC:
13
AN:
1459008
Hom.:
0
Cov.:
30
AF XY:
0.00000964
AC XY:
7
AN XY:
726084
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000108
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
31
Alfa
AF:
0.0000987
Hom.:
0
Bravo
AF:
0.00000756

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:3Uncertain:8Benign:1
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1Uncertain:1Benign:1
Sep 29, 2017
Counsyl
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Nov 26, 2024
Myriad Genetics, Inc.
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing. 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]. -

Oct 18, 2023
Baylor Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Lynch syndrome Pathogenic:1Uncertain:1
Jun 21, 2019
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
Significance: Likely pathogenic
Review Status: reviewed by expert panel
Collection Method: curation

Interrupts canonical donor splice site -

Jun 17, 2024
All of Us Research Program, National Institutes of Health
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: 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 also 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 evidence is necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

not provided Uncertain:2
Mar 01, 2023
Revvity Omics, Revvity
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 20, 2023
GeneDx
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: 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) -

Hereditary cancer-predisposing syndrome Uncertain:2
May 09, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: 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. Based on the available evidence, the clinical significance of this variant remains unclear. -

May 12, 2023
Color Diagnostics, LLC DBA Color Health
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: 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. -

Muir-Torré syndrome;C1333991:Colorectal cancer, hereditary nonpolyposis, type 2;C5399763:Mismatch repair cancer syndrome 1 Pathogenic:1
Oct 31, 2018
Fulgent Genetics, Fulgent Genetics
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not specified Uncertain:1
Feb 27, 2022
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: 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. -

Hereditary nonpolyposis colorectal neoplasms Uncertain:1
Dec 10, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: 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 (internal data). 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. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.63
D
BayesDel_noAF
Pathogenic
0.26
CADD
Pathogenic
32
DANN
Uncertain
0.99
Eigen
Pathogenic
1.1
Eigen_PC
Pathogenic
0.99
FATHMM_MKL
Pathogenic
0.99
D
GERP RS
5.3

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
SpliceAI score (max)
1.0
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.33
Position offset: 6
DS_AL_spliceai
1.0
Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs267607871; hg19: chr3-37090006; API