chr3-37001057-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP6_Strong

The NM_000249.4(MLH1):​c.306+4A>G variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0000332 in 1,564,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000035 ( 0 hom. )

Consequence

MLH1
NM_000249.4 splice_region, intron

Scores

2
Splicing: ADA: 0.9950
2

Clinical Significance

Uncertain significance reviewed by expert panel U:10B:2

Conservation

PhyloP100: 6.51
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 Likely_benign. Variant got -4 ACMG points.

BP6
Variant 3-37001057-A-G is Benign according to our data. Variant chr3-37001057-A-G is described in ClinVar as [Uncertain_significance]. Clinvar id is 90147.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=10, Likely_benign=2}. Variant chr3-37001057-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MLH1NM_000249.4 linkc.306+4A>G splice_region_variant, intron_variant Intron 3 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.306+4A>G splice_region_variant, intron_variant Intron 3 of 18 1 NM_000249.4 ENSP00000231790.3 P40692-1

Frequencies

GnomAD3 genomes
AF:
0.0000131
AC:
2
AN:
152192
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000119
AC:
3
AN:
251334
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135850
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:
0.0000264
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000354
AC:
50
AN:
1412134
Hom.:
0
Cov.:
25
AF XY:
0.0000241
AC XY:
17
AN XY:
705532
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:
0.0000469
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000131
AC:
2
AN:
152192
Hom.:
0
Cov.:
32
AF XY:
0.0000134
AC XY:
1
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000113
EpiCase
AF:
0.00
EpiControl
AF:
0.000119

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:10Benign:2
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:3
Uncertain significance, criteria provided, single submitterclinical testingColor Diagnostics, LLC DBA Color HealthApr 28, 2023This variant causes an A to G nucleotide substitution at the +4 position of intron 3 of the MLH1 gene. To our knowledge, functional studies have not been reported for this variant. Splice site prediction tools are inconclusive regarding the impact of this variant on RNA splicing. This variant has been reported in individuals affected with endometrial cancer and breast cancer (PMID: 26898890, 32634176). This variant has been identified in 3/251334 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitterclinical testingGeneKor MSAAug 01, 2018- -
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 26, 2024The c.306+4A>G intronic variant results from an A to G substitution 4 nucleotides after coding exon 3 in the MLH1 gene. This alteration has been reported in 1/1197 individuals from Greece, Romania, and Turkey undergoing evaluation for inherited cancer predisposition (Tsaousis GN et al. BMC Cancer, 2019 Jun;19:535). This variant was also observed in 1/287 patients with hereditary breast and/or ovarian cancer (Caminsky NG et al. Hum Mutat, 2016 07;37:640-52). Furthermore, this variant was identified in 1/199 endometrial cancer patients (Singh AK et al. PLoS One, 2020 Jul;15(7):e0235613). In a functional RNA study, this variant was associated with in-frame exon 3 skipping and activation of a cryptic donor site in exon 3; however, splicing was tested using a mini gene assay and patient RNA was not analyzed (Tournier I et al. Hum. Mutat. 2008 Dec;29:1412-24). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). However, this alteration has been detected in many probands who do not have a personal or family history that is consistent with or suggestive of hereditary nonpolyposis colorectal cancer (HNPCC)/Lynch syndrome and one of these individuals was diagnosed with microsatellite stable colorectal cancer that demonstrated normal mismatch repair protein expression by immunohistochemistry (Ambry internal data). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -
Lynch syndrome Uncertain:2
Uncertain significance, reviewed by expert panelcurationInternational Society for Gastrointestinal Hereditary Tumours (InSiGHT)Oct 18, 2018Insufficient evidence: splicing not tested in patient RNA -
Uncertain significance, criteria provided, single submitterclinical testingAll of Us Research Program, National Institutes of HealthMar 24, 2024This variant causes an A to G nucleotide substitution at the +4 position of intron 3 of the MLH1 gene. To our knowledge, functional studies have not been reported for this variant. Splice site prediction tools are inconclusive regarding the impact of this variant on RNA splicing. This variant has been reported in individuals affected with endometrial cancer and breast cancer (PMID: 26898890, 32634176). This variant has been identified in 3/251334 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient 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
Uncertain significance, criteria provided, single submitterclinical testingQuest Diagnostics Nichols Institute San Juan CapistranoSep 09, 2020- -
Uncertain significance, criteria provided, single submitterclinical testingGeneDxNov 14, 2022Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Observed in individuals with suspected Lynch syndrome or familial breast/ovarian cancer (Tournier et al., 2008; Caminsky et al., 2016; Singh et al., 2020); Published functional studies demonstrate an impact on splicing in an ex vivo assay; however, these findings were not confirmed in patient RNA (Tournier et al., 2008); This variant is associated with the following publications: (PMID: 25525159, 26898890, 20858721, 31159747, 18561205, 32634176) -
Colorectal cancer, hereditary nonpolyposis, type 2 Uncertain:1Benign:1
Likely benign, criteria provided, single submitterclinical testingMyriad Genetics, Inc.Nov 13, 2023This 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]. -
Uncertain significance, criteria provided, single submitterclinical testingBaylor GeneticsOct 26, 2023- -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpDec 11, 2023Variant summary: MLH1 c.306+4A>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Consensus agreement among computation tools predict no significant impact on normal splicing. At least one publication reports experimental evidence that this variant affects mRNA splicing, resulting in activation of a cryptic donor site in an ex vivo assay (Tournier_2008). However, this was not confirmed in patient RNA. The variant allele was found at a frequency of 1.2e-05 in 251334 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.306+4A>G has been reported in the literature in individuals affected with a personal or family history of cancer without strong evidence of causality (e.g. Grant_2015, Caminsky_2016, Ring_2016, Tsoaousis_2019, Singh_2020, Bhai_2021). These reports do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. The following publications have been ascertained in the context of this evaluation (PMID: 18561205, 25479140, 26898890, 27443514, 31159747, 32634176, 34326862). Seven submitters, including an expert panel, have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Breast and/or ovarian cancer Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingCHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern OntarioJan 06, 2023- -
Hereditary nonpolyposis colorectal neoplasms Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 04, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.22
CADD
Benign
16
DANN
Benign
0.96

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
0.99
dbscSNV1_RF
Pathogenic
0.78
SpliceAI score (max)
0.61
Details are displayed if max score is > 0.2
DS_DL_spliceai
0.61
Position offset: -4

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: rs267607733; hg19: chr3-37042548; API